Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167993.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_25, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 17943224
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 94000 characters in sequence are not A, C, G, or T
File 16 of 100
Found at i:2917435 original size:2 final size:2
Alignment explanation
Indices: 2917422--2917455 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
2917412 GAATTTTTCC
*
2917422 AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2917456 TCTAGTGACA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:2919649 original size:3 final size:3
Alignment explanation
Indices: 2919643--2919671 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
2919633 TTTTTTTTCT
2919643 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
2919672 TTGTAATCTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:2920741 original size:33 final size:33
Alignment explanation
Indices: 2920704--2920769 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
2920694 TGAATATGAG
** *
2920704 TATGAAAATCTGAACCATTAAATGTATGAAAAA
1 TATGAAAATCCAAACCATTAAATATATGAAAAA
2920737 TATGAAAATCCAAACCATTAAATATATGAAAAA
1 TATGAAAATCCAAACCATTAAATATATGAAAAA
2920770 AATTAAAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.55, C:0.11, G:0.09, T:0.26
Consensus pattern (33 bp):
TATGAAAATCCAAACCATTAAATATATGAAAAA
Found at i:2926982 original size:22 final size:22
Alignment explanation
Indices: 2926957--2927005 Score: 59
Period size: 21 Copynumber: 2.3 Consensus size: 22
2926947 ATAAAAAAAA
2926957 TTTAAAAT-TTATTTATTTATT-T
1 TTTAAAATATTA-TT-TTTATTAT
2926979 TTT-AAATATTATTTTTATTAT
1 TTTAAAATATTATTTTTATTAT
2927000 TTTAAA
1 TTTAAA
2927006 TTTTTATCAT
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
20 6 0.25
21 10 0.42
22 8 0.33
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (22 bp):
TTTAAAATATTATTTTTATTAT
Found at i:2938481 original size:21 final size:20
Alignment explanation
Indices: 2938453--2938491 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
2938443 TGATTATCGT
* *
2938453 TTTAATATCATTTGTAAAGA
1 TTTAATATAACTTGTAAAGA
2938473 TTTACATATAACTTGTAAA
1 TTTA-ATATAACTTGTAAA
2938492 ATATAATTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.41, C:0.08, G:0.08, T:0.44
Consensus pattern (20 bp):
TTTAATATAACTTGTAAAGA
Found at i:2939260 original size:34 final size:31
Alignment explanation
Indices: 2939153--2939276 Score: 106
Period size: 34 Copynumber: 3.9 Consensus size: 31
2939143 TATCCTATGT
* * **
2939153 ATTATTTATTTATTTATTAGTACTATTTATTA
1 ATTATATATTTATTT-TTATTTTTATTTATTA
*
2939185 A-TATATATATATTTTTATTTTTATTTATTA
1 ATTATATATTTATTTTTATTTTTATTTATTA
* *
2939215 TTTATTTTATTTATTTTTGTATTTTTATTTATCTA
1 ATTA-TATATTTA-TTTT-TATTTTTATTTAT-TA
* * *
2939250 ATTATATATTTGTTATTATTATTATTT
1 ATTATATATTTATTTTTATTTTTATTT
2939277 GTTTTTTTAT
Statistics
Matches: 74, Mismatches: 13, Indels: 10
0.76 0.13 0.10
Matches are distributed among these distances:
30 13 0.18
31 13 0.18
32 17 0.23
33 7 0.09
34 19 0.26
35 5 0.07
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.68
Consensus pattern (31 bp):
ATTATATATTTATTTTTATTTTTATTTATTA
Found at i:2939278 original size:44 final size:42
Alignment explanation
Indices: 2939194--2939291 Score: 121
Period size: 44 Copynumber: 2.3 Consensus size: 42
2939184 AATATATATA
*
2939194 TATTTTTATTT-T-TATTTATTATTTATTTTATTTATTTTTG
1 TATTTTTATTTATCTAATTATTATTTATTTTATTTATTTTTG
*
2939234 TATTTTTATTTATCTAATTATATATTTGTTATTA-TTATTATTTG
1 TATTTTTATTTATCTAATTAT-TATTTATT-TTATTTATT-TTTG
*
2939278 TTTTTTTATTTATC
1 TATTTTTATTTATC
2939292 CTATAATATT
Statistics
Matches: 50, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
40 11 0.22
41 1 0.02
42 6 0.12
43 12 0.24
44 20 0.40
ACGTcount: A:0.22, C:0.02, G:0.03, T:0.72
Consensus pattern (42 bp):
TATTTTTATTTATCTAATTATTATTTATTTTATTTATTTTTG
Found at i:2939319 original size:36 final size:34
Alignment explanation
Indices: 2939279--2939347 Score: 93
Period size: 34 Copynumber: 2.0 Consensus size: 34
2939269 TATTATTTGT
*
2939279 TTTTTTATTTATCCTATAATATTTTTTTGATTTATC
1 TTTTTTAATTAT-CTATAAT-TTTTTTTGATTTATC
* *
2939315 TTTTTTAATTATCTATTATTTTTTTTTATTTAT
1 TTTTTTAATTATCTATAATTTTTTTTGATTTAT
2939348 TTGATTTTTA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
34 13 0.43
35 6 0.20
36 11 0.37
ACGTcount: A:0.22, C:0.06, G:0.01, T:0.71
Consensus pattern (34 bp):
TTTTTTAATTATCTATAATTTTTTTTGATTTATC
Found at i:2939354 original size:5 final size:4
Alignment explanation
Indices: 2939154--2939354 Score: 63
Period size: 4 Copynumber: 51.5 Consensus size: 4
2939144 ATCCTATGTA
* * * *
2939154 TTAT TTAT TTAT TTA- TTAGT ACTAT TTAT TAAT ATAT ATAT ATT-T TTA-
1 TTAT TTAT TTAT TTAT TTA-T -TTAT TTAT TTAT TTAT TTAT -TTAT TTAT
2939202 TT-T TTAT TTA- TTAT TTATT TTAT TTAT TT-T TGTA- TT-T TTAT TTAT
1 TTAT TTAT TTAT TTAT TTA-T TTAT TTAT TTAT T-TAT TTAT TTAT TTAT
* * * * * *
2939247 CTAA TTAT ATAT TT-G TTA- TTA- TTA- TTAT TTGT TTTT TTAT TTAT
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT
* * * * * *
2939291 CCTAT AATAT TTTT TTGAT TTAT CTTTT TTAA TTAT CTA- TTAT TT-T
1 -TTAT -TTAT TTAT TT-AT TTAT -TTAT TTAT TTAT TTAT TTAT TTAT
2939337 TT-T TTAT TTAT TTGAT TT
1 TTAT TTAT TTAT TT-AT TT
2939355 TTATTTTGGA
Statistics
Matches: 148, Mismatches: 28, Indels: 41
0.68 0.13 0.19
Matches are distributed among these distances:
3 36 0.24
4 88 0.59
5 22 0.15
6 2 0.01
ACGTcount: A:0.25, C:0.03, G:0.03, T:0.69
Consensus pattern (4 bp):
TTAT
Found at i:2940173 original size:11 final size:11
Alignment explanation
Indices: 2940145--2940192 Score: 57
Period size: 11 Copynumber: 4.5 Consensus size: 11
2940135 CGCTTCAGGT
2940145 TTTATTTTTT-
1 TTTATTTTTTA
*
2940155 TTGAATTTTTTA
1 TT-TATTTTTTA
2940167 TTTA--TTTTA
1 TTTATTTTTTA
2940176 TTTATTTTTTA
1 TTTATTTTTTA
2940187 TTTATT
1 TTTATT
2940193 AGATTAGGTT
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
9 9 0.28
10 2 0.06
11 19 0.59
12 2 0.06
ACGTcount: A:0.19, C:0.00, G:0.02, T:0.79
Consensus pattern (11 bp):
TTTATTTTTTA
Found at i:2940182 original size:20 final size:21
Alignment explanation
Indices: 2940145--2940192 Score: 71
Period size: 20 Copynumber: 2.3 Consensus size: 21
2940135 CGCTTCAGGT
*
2940145 TTTATTTTTTTTGAATTTTTTA
1 TTTATTTTATTT-AATTTTTTA
2940167 TTTATTTTATTT-ATTTTTTA
1 TTTATTTTATTTAATTTTTTA
2940187 TTTATT
1 TTTATT
2940193 AGATTAGGTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 14 0.56
22 11 0.44
ACGTcount: A:0.19, C:0.00, G:0.02, T:0.79
Consensus pattern (21 bp):
TTTATTTTATTTAATTTTTTA
Found at i:2940231 original size:11 final size:11
Alignment explanation
Indices: 2940215--2940279 Score: 62
Period size: 11 Copynumber: 5.8 Consensus size: 11
2940205 GTTAATATTT
*
2940215 TTTTATCTTTA
1 TTTTATTTTTA
2940226 TTTTATTTTTA
1 TTTTATTTTTA
2940237 TTTT-TGTTTTA
1 TTTTAT-TTTTA
* *
2940248 CTTT-TCTTTA
1 TTTTATTTTTA
2940258 TTTTATTTTTTA
1 TTTTA-TTTTTA
2940270 TTTTTATTTT
1 -TTTTATTTT
2940280 GTTTTATTAT
Statistics
Matches: 45, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
10 8 0.18
11 23 0.51
12 9 0.20
13 5 0.11
ACGTcount: A:0.14, C:0.05, G:0.02, T:0.80
Consensus pattern (11 bp):
TTTTATTTTTA
Found at i:2940232 original size:5 final size:5
Alignment explanation
Indices: 2940215--2940287 Score: 53
Period size: 5 Copynumber: 14.4 Consensus size: 5
2940205 GTTAATATTT
* *
2940215 TTTTA TCTTTA TTTTA TTTTTA TTTTTG TTTTA CTTTT- CTTTA TTTTA
1 TTTTA T-TTTA TTTTA -TTTTA -TTTTA TTTTA -TTTTA TTTTA TTTTA
* *
2940263 TTTT- TTAT- TTTTA TTTTG TTTTA TT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TT
2940288 ATTCAATTTT
Statistics
Matches: 55, Mismatches: 8, Indels: 10
0.75 0.11 0.14
Matches are distributed among these distances:
4 9 0.16
5 27 0.49
6 19 0.35
ACGTcount: A:0.14, C:0.04, G:0.03, T:0.79
Consensus pattern (5 bp):
TTTTA
Found at i:2940235 original size:6 final size:6
Alignment explanation
Indices: 2940214--2940279 Score: 55
Period size: 6 Copynumber: 10.7 Consensus size: 6
2940204 AGTTAATATT
* * *
2940214 TTTTTA TCTTTA -TTTTA TTTTTA TTTTT- GTTTTA CTTTTCTT TATTTTA
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA -TTTT-TA T-TTTTA
2940263 TTTTTTA TTTTTA TTTT
1 -TTTTTA TTTTTA TTTT
2940280 GTTTTATTAT
Statistics
Matches: 48, Mismatches: 6, Indels: 12
0.73 0.09 0.18
Matches are distributed among these distances:
5 8 0.17
6 25 0.52
7 10 0.21
8 5 0.10
ACGTcount: A:0.14, C:0.05, G:0.02, T:0.80
Consensus pattern (6 bp):
TTTTTA
Found at i:2940531 original size:62 final size:58
Alignment explanation
Indices: 2940290--2940838 Score: 570
Period size: 62 Copynumber: 9.1 Consensus size: 58
2940280 GTTTTATTAT
* * * *
2940290 TCAATTTT-CTT-TAAATAAAA-ATAAAAAATATATATTTTTGGGGAAAAGTTGAAAGTA
1 TCAATTTTCCTTAAAAATAAAATTTAAAAAA-A-ATTTTTTTGAGGAAAAGTTGAAAGTA
*
2940347 TCAATTTTCCTTAAAAATAAAATTTCAAAAAAAAAGGTTTTTTGAGGAAAAGTTGAAAGTA
1 TCAATTTTCCTTAAAAATAAAATTT--AAAAAAAA-TTTTTTTGAGGAAAAGTTGAAAGTA
* ** *
2940408 TCAATTTTCCTTGAAAATCAAAATTT-TCAAAAATATTTTTGAGGAAAAGTTGAAAGTA
1 TCAATTTTCCTTAAAAAT-AAAATTTAAAAAAAATTTTTTTGAGGAAAAGTTGAAAGTA
** *
2940466 TCAATTTTTTTTAAAAATAAAA-TTAAAAAAAAGGGTGTTTTTTTTAGGAAAAGTTGAAAGTA
1 TCAATTTTCCTTAAAAATAAAATTTAAAAAAAA-----TTTTTTTGAGGAAAAGTTGAAAGTA
*
2940528 TCAATTTTTCTTAAAAATAAAATTTCAAAAAAATGAGTTTTTTTGAGGAAAAGTTGAAAGTA
1 TCAATTTTCCTTAAAAATAAAATTT-AAAAAAA--A-TTTTTTTGAGGAAAAGTTGAAAGTA
* * ** * *
2940590 TCAATTTTCCTTGAAAATCAAAGTTT-CCAAAAATATTTTTGAGAAAAAGTTGAAAGTA
1 TCAATTTTCCTTAAAAAT-AAAATTTAAAAAAAATTTTTTTGAGGAAAAGTTGAAAGTA
* *
2940648 TCAATTTTCCTTAAAAATAAATTTTCAAAAAAAGATTTTTTTTAGGAAAAGTTGAAAGTA
1 TCAATTTTCCTTAAAAATAAAATTT-AAAAAAA-ATTTTTTTGAGGAAAAGTTGAAAGTA
* * * *
2940708 TCAATTTTCCTTGAAAATCAAAATTTTCAAAAAAATATTTCTTGGGGAAAAGTTGAAAGTA
1 TCAATTTTCCTTAAAAAT-AAAA-TTTAAAAAAAAT-TTTTTTGAGGAAAAGTTGAAAGTA
* * * *
2940769 TCAATTTTTCTTAAAAAAAATCAATTTAAAAAAAATCAATTTTTGGGGAAAAGTTGAAAGTA
1 TCAATTTTCCTTAAAAATAA--AATTTAAAAAAAAT--TTTTTTGAGGAAAAGTTGAAAGTA
2940831 TCAATTTT
1 TCAATTTT
2940839 TCCTGCACAA
Statistics
Matches: 420, Mismatches: 45, Indels: 49
0.82 0.09 0.10
Matches are distributed among these distances:
56 2 0.00
57 23 0.05
58 81 0.19
59 18 0.04
60 46 0.11
61 100 0.24
62 134 0.32
63 8 0.02
64 7 0.02
66 1 0.00
ACGTcount: A:0.45, C:0.07, G:0.12, T:0.36
Consensus pattern (58 bp):
TCAATTTTCCTTAAAAATAAAATTTAAAAAAAATTTTTTTGAGGAAAAGTTGAAAGTA
Found at i:2940640 original size:182 final size:177
Alignment explanation
Indices: 2940331--2940840 Score: 702
Period size: 182 Copynumber: 2.8 Consensus size: 177
2940321 ATATTTTTGG
*
2940331 GGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAAATTTCAAAAAAAAAGGTTTTTTGAGGAA
1 GGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAAATTTCAAAAAAATA-GTTTTTTGAGGAA
*
2940396 AAGTTGAAAGTATCAATTTTCCTTGAAAATCAAAATTTTCAAAAATATTTTTGAGGAAAAGTTGA
65 AAGTTGAAAGTATCAATTTTCCTTGAAAATC-AAATTTACAAAAATATTTTTGAGGAAAAGTTGA
* *
2940461 AAGTATCAATTTTTTTTAAAAATAAA-ATTAAAAAAAAGGGTGTTTTTTTTA
129 AAGTATCAATTTTTCTTAAAAATAAATATTAAAAAAAA--G-ATTTTTTTTA
*
2940512 GGAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAAATTTCAAAAAAATGAGTTTTTTTGAGGA
1 GGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAAATTTCAAAAAAAT-AG-TTTTTTGAGGA
* *
2940577 AAAGTTGAAAGTATCAATTTTCCTTGAAAATCAAAGTTTCCAAAAATATTTTTGAGAAAAAGTTG
64 AAAGTTGAAAGTATCAATTTTCCTTGAAAATCAAA-TTTACAAAAATATTTTTGAGGAAAAGTTG
* * *
2940642 AAAGTATCAATTTTCCTTAAAAATAAATTTTCAAAAAAAGATTTTTTTTA
128 AAAGTATCAATTTTTCTTAAAAATAAATATTAAAAAAAAGATTTTTTTTA
* * *
2940692 GGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATCAAAATTTTCAAAAAAATA-TTTCTTGGGGA
1 GGAAAAGTTGAAAGTATCAATTTTCCTTAAAAAT-AAAA-TTTCAAAAAAATAGTTTTTTGAGGA
* * * *
2940756 AAAGTTGAAAGTATCAATTTTTCTTAAAAAAAATC-AATTTAAAAAAAATCAATTTTTGGGGAAA
64 AAAGTTGAAAGTATCAATTTTCCTT---GAAAATCAAATTT-ACAAAAAT--ATTTTTGAGGAAA
2940820 AGTTGAAAGTATCAATTTTTC
123 AGTTGAAAGTATCAATTTTTC
2940841 CTGCACAAGA
Statistics
Matches: 297, Mismatches: 20, Indels: 22
0.88 0.06 0.06
Matches are distributed among these distances:
179 33 0.11
180 44 0.15
181 66 0.22
182 114 0.38
183 40 0.13
ACGTcount: A:0.45, C:0.07, G:0.13, T:0.36
Consensus pattern (177 bp):
GGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAAATTTCAAAAAAATAGTTTTTTGAGGAAA
AGTTGAAAGTATCAATTTTCCTTGAAAATCAAATTTACAAAAATATTTTTGAGGAAAAGTTGAAA
GTATCAATTTTTCTTAAAAATAAATATTAAAAAAAAGATTTTTTTTA
Found at i:2940802 original size:16 final size:15
Alignment explanation
Indices: 2940779--2940810 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
2940769 TCAATTTTTC
2940779 TTAAAAAAAATCAAT
1 TTAAAAAAAATCAAT
2940794 TTAAAAAAAATCAAT
1 TTAAAAAAAATCAAT
2940809 TT
1 TT
2940811 TTGGGGAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.62, C:0.06, G:0.00, T:0.31
Consensus pattern (15 bp):
TTAAAAAAAATCAAT
Found at i:2951293 original size:29 final size:29
Alignment explanation
Indices: 2951253--2951345 Score: 143
Period size: 31 Copynumber: 3.1 Consensus size: 29
2951243 ACTACGCTTG
2951253 AAAAAA-AATGAAAAAATGAGAAAATGAA
1 AAAAAATAATGAAAAAATGAGAAAATGAA
2951281 AAAAAATAATGAAAAAATGAGAAAATGAAAA
1 AAAAAATAATGAAAAAATGAGAAAATG--AA
*
2951312 AAAAAATGATGAAAAAATGAGAAAAATGAA
1 AAAAAATAATGAAAAAATGAG-AAAATGAA
2951342 AAAA
1 AAAA
2951346 TGGAAAAAAT
Statistics
Matches: 60, Mismatches: 1, Indels: 6
0.90 0.01 0.09
Matches are distributed among these distances:
28 6 0.10
29 20 0.33
30 6 0.10
31 22 0.37
32 6 0.10
ACGTcount: A:0.74, C:0.00, G:0.14, T:0.12
Consensus pattern (29 bp):
AAAAAATAATGAAAAAATGAGAAAATGAA
Found at i:2951317 original size:31 final size:30
Alignment explanation
Indices: 2951253--2951393 Score: 169
Period size: 29 Copynumber: 4.5 Consensus size: 30
2951243 ACTACGCTTG
2951253 AAAAAAAATGAAAAAATGAGAAAATG-AAA
1 AAAAAAAATGAAAAAATGAGAAAATGAAAA
*
2951282 AAAAATAATGAAAAAATGAGAAAATGAAAA
1 AAAAAAAATGAAAAAATGAGAAAATGAAAA
*
2951312 AAAAAATGATGAAAAAATGAGAAAAATGAAAA
1 AAAAAA-AATGAAAAAATGAG-AAAATGAAAA
* *
2951344 AATGGAAAAAATGAAAAAAT-AAAAAAAGAAAA
1 AA---AAAAAATGAAAAAATGAGAAAATGAAAA
2951376 AAAGAAAAAGTGAAAAAA
1 AAA-AAAAA-TGAAAAAA
2951394 GAGGACTTAA
Statistics
Matches: 98, Mismatches: 6, Indels: 14
0.83 0.05 0.12
Matches are distributed among these distances:
29 26 0.27
30 13 0.13
31 21 0.21
32 23 0.23
33 1 0.01
34 10 0.10
35 4 0.04
ACGTcount: A:0.75, C:0.00, G:0.14, T:0.11
Consensus pattern (30 bp):
AAAAAAAATGAAAAAATGAGAAAATGAAAA
Found at i:2951394 original size:9 final size:8
Alignment explanation
Indices: 2951255--2951393 Score: 146
Period size: 8 Copynumber: 17.8 Consensus size: 8
2951245 TACGCTTGAA
2951255 AAAAAATG
1 AAAAAATG
2951263 AAAAAATG
1 AAAAAATG
*
2951271 AGAAAATG
1 AAAAAATG
2951279 -AAAAA--
1 AAAAAATG
*
2951284 AAATAATG
1 AAAAAATG
2951292 AAAAAATG
1 AAAAAATG
*
2951300 AGAAAATG
1 AAAAAATG
2951308 AAAAAA--
1 AAAAAATG
*
2951314 AAAATGATG
1 AAAA-AATG
2951323 AAAAAATG
1 AAAAAATG
2951331 AGAAAAATG
1 A-AAAAATG
2951340 AAAAAATGG
1 AAAAAAT-G
2951349 AAAAAATG
1 AAAAAATG
2951357 AAAAAAT-
1 AAAAAATG
*
2951364 AAAAAAAG
1 AAAAAATG
*
2951372 AAAAAAAG
1 AAAAAATG
*
2951380 AAAAAGTG
1 AAAAAATG
2951388 AAAAAA
1 AAAAAA
2951394 GAGGACTTAA
Statistics
Matches: 110, Mismatches: 12, Indels: 18
0.79 0.09 0.13
Matches are distributed among these distances:
6 8 0.07
7 11 0.10
8 71 0.65
9 20 0.18
ACGTcount: A:0.75, C:0.00, G:0.14, T:0.11
Consensus pattern (8 bp):
AAAAAATG
Found at i:2952462 original size:43 final size:41
Alignment explanation
Indices: 2952390--2952521 Score: 183
Period size: 43 Copynumber: 3.1 Consensus size: 41
2952380 ATGATTGTCA
2952390 AGGAGCAATTTATTTTTCAAAGTCGTGGTGCCTCTGTTTAG
1 AGGAGCAATTTATTTTTCAAAGTCGTGGTGCCTCTGTTTAG
** *
2952431 AGGAGCAATTTACTTTCCCAAAAGTCGTGGTGTCTCTGTTTAG
1 AGGAGCAATTTA-TTTTTC-AAAGTCGTGGTGCCTCTGTTTAG
* * *
2952474 AGGAGCAATTTATTTTTTCAAAGTCGTTGAGCTTCTGTTTAG
1 AGGAGCAATTTA-TTTTTCAAAGTCGTGGTGCCTCTGTTTAG
2952516 AGGAGC
1 AGGAGC
2952522 TTCGATTAAA
Statistics
Matches: 79, Mismatches: 10, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
41 12 0.15
42 29 0.37
43 38 0.48
ACGTcount: A:0.23, C:0.15, G:0.24, T:0.37
Consensus pattern (41 bp):
AGGAGCAATTTATTTTTCAAAGTCGTGGTGCCTCTGTTTAG
Found at i:2952782 original size:12 final size:11
Alignment explanation
Indices: 2952742--2952908 Score: 64
Period size: 11 Copynumber: 14.9 Consensus size: 11
2952732 GGTAAGTCCA
2952742 ATTT-TATTTT
1 ATTTATATTTT
*
2952752 -TGTTATTTTTT
1 AT-TTATATTTT
2952763 ATTT-TATTTT
1 ATTTATATTTT
2952773 ATTCTATATTTT
1 ATT-TATATTTT
2952785 ATGTATATATTTT
1 AT-T-TATATTTT
* **
2952798 CCTTTATATCCT
1 -ATTTATATTTT
*
2952810 ATGTAT-TATTT
1 ATTTATAT-TTT
2952821 ATTTAT-TTATT
1 ATTTATATT-TT
2952832 A-TTACTA-TTT
1 ATTTA-TATTTT
* *
2952842 ATTAATATATAT
1 ATTTATAT-TTT
2952854 ATTT-TATTTTT
1 ATTTATA-TTTT
*
2952865 ATTTTTA-TTT
1 ATTTATATTTT
*
2952875 ATTTTTTATTTT
1 A-TTTATATTTT
*
2952887 ATTTATTTTTGT
1 ATTTATATTT-T
*
2952899 ATTTTTATTT
1 ATTTATATTT
2952909 ATCTAATTAT
Statistics
Matches: 119, Mismatches: 19, Indels: 36
0.68 0.11 0.21
Matches are distributed among these distances:
9 1 0.01
10 24 0.20
11 47 0.39
12 36 0.30
13 10 0.08
14 1 0.01
ACGTcount: A:0.23, C:0.04, G:0.02, T:0.71
Consensus pattern (11 bp):
ATTTATATTTT
Found at i:2952824 original size:4 final size:4
Alignment explanation
Indices: 2952815--2952910 Score: 60
Period size: 4 Copynumber: 24.0 Consensus size: 4
2952805 ATCCTATGTA
* * *
2952815 TTAT TTAT TTAT TTA- TTAT TACTAT TTAT TAAT ATAT ATATT TTAT TT-T
1 TTAT TTAT TTAT TTAT TTAT T--TAT TTAT TTAT TTAT TTA-T TTAT TTAT
*
2952864 TATTT TTAT TTAT TT-T TTATT TTAT TTAT TT-T TGTA- TT-T TTAT TTAT
1 T-TAT TTAT TTAT TTAT TTA-T TTAT TTAT TTAT T-TAT TTAT TTAT TTAT
2952911 CTAATTATAT
Statistics
Matches: 75, Mismatches: 5, Indels: 24
0.72 0.05 0.23
Matches are distributed among these distances:
3 13 0.17
4 49 0.65
5 9 0.12
6 4 0.05
ACGTcount: A:0.25, C:0.01, G:0.01, T:0.73
Consensus pattern (4 bp):
TTAT
Found at i:2952842 original size:17 final size:17
Alignment explanation
Indices: 2952813--2952940 Score: 83
Period size: 16 Copynumber: 7.6 Consensus size: 17
2952803 ATATCCTATG
2952813 TATTATTTATTTATTTAT
1 TATTA-TTATTTATTTAT
* *
2952831 TATTACTATTTA-TTAA
1 TATTATTATTTATTTAT
2952847 TA-TATATATTTTATTT-T
1 TATTAT-TA-TTTATTTAT
* *
2952864 TATTTTTATTTATTTTT
1 TATTATTATTTATTTAT
2952881 TATT-TTATTTATTT-T
1 TATTATTATTTATTTAT
*
2952896 T-GTATT-TTTATTTAT
1 TATTATTATTTATTTAT
* *
2952911 CTAATTATATATCT-GTTAT
1 -T-ATTAT-TATTTATTTAT
2952930 TATTATTATTT
1 TATTATTATTT
2952941 GTTTTTTTAT
Statistics
Matches: 88, Mismatches: 10, Indels: 26
0.71 0.08 0.21
Matches are distributed among these distances:
14 8 0.09
15 7 0.08
16 29 0.33
17 24 0.27
18 13 0.15
19 5 0.06
20 2 0.02
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.70
Consensus pattern (17 bp):
TATTATTATTTATTTAT
Found at i:2952861 original size:21 final size:21
Alignment explanation
Indices: 2952813--2952862 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
2952803 ATATCCTATG
* *
2952813 TATTATTTATTTATTTATTAT
1 TATTATTTATTAATATATTAT
*
2952834 TACTATTTATTAATATATATAT
1 TATTATTTATTAATATAT-TAT
2952856 T-TTATTT
1 TATTATTT
2952863 TTATTTTTAT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (21 bp):
TATTATTTATTAATATATTAT
Found at i:2952864 original size:6 final size:6
Alignment explanation
Indices: 2952855--2952908 Score: 60
Period size: 6 Copynumber: 9.3 Consensus size: 6
2952845 AATATATATA
* *
2952855 TTTTAT TTTTAT TTTTAT TTAT-T TTTTA- TTTTAT TTATT-T TTGTAT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TT-TTAT TTTTAT
2952901 TTTTAT TT
1 TTTTAT TT
2952909 ATCTAATTAT
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
5 10 0.25
6 28 0.70
7 2 0.05
ACGTcount: A:0.17, C:0.00, G:0.02, T:0.81
Consensus pattern (6 bp):
TTTTAT
Found at i:2952881 original size:23 final size:24
Alignment explanation
Indices: 2952819--2952908 Score: 78
Period size: 23 Copynumber: 3.7 Consensus size: 24
2952809 TATGTATTAT
* **
2952819 TTATTTATTTATTATTACTATTTA
1 TTATTTATTTTTTATTTTTATTTA
*
2952843 TTAATATATATATTTTATTTTTATTT-
1 TT-AT-T-TATTTTTTATTTTTATTTA
2952869 TTATTTATTTTTTA-TTTTATTTA
1 TTATTTATTTTTTATTTTTATTTA
*
2952892 TT-TTTGTATTTTTATTT
1 TTATTTAT-TTTTTATTT
2952909 ATCTAATTAT
Statistics
Matches: 54, Mismatches: 6, Indels: 12
0.75 0.08 0.17
Matches are distributed among these distances:
22 12 0.22
23 16 0.30
24 5 0.09
25 4 0.07
26 3 0.06
27 14 0.26
ACGTcount: A:0.24, C:0.01, G:0.01, T:0.73
Consensus pattern (24 bp):
TTATTTATTTTTTATTTTTATTTA
Found at i:2953003 original size:13 final size:14
Alignment explanation
Indices: 2952987--2953020 Score: 52
Period size: 13 Copynumber: 2.4 Consensus size: 14
2952977 TCTTTTCTAA
2952987 TTATTTATTT-TTT
1 TTATTTATTTATTT
2953000 TTATTTATTTGATTT
1 TTATTTATTT-ATTT
2953015 TTATTT
1 TTATTT
2953021 TGAAAAGTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 10 0.53
15 9 0.47
ACGTcount: A:0.18, C:0.00, G:0.03, T:0.79
Consensus pattern (14 bp):
TTATTTATTTATTT
Found at i:2953885 original size:6 final size:6
Alignment explanation
Indices: 2953864--2953936 Score: 58
Period size: 6 Copynumber: 11.7 Consensus size: 6
2953854 AGTTAATATT
* * * *
2953864 TTTTTA TCTTTA -TTTTA TTTTTA TTTTTG TTTTGCTT TTCTTTA TTTTATT
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTT--TA TT-TTTA TTTT-TA
*
2953915 TTTTTA TTTTCA TTTTTA TTTT
1 TTTTTA TTTTTA TTTTTA TTTT
2953937 GTTTTATTAT
Statistics
Matches: 53, Mismatches: 9, Indels: 10
0.74 0.12 0.14
Matches are distributed among these distances:
5 4 0.08
6 36 0.68
7 8 0.15
8 3 0.06
9 2 0.04
ACGTcount: A:0.12, C:0.05, G:0.03, T:0.79
Consensus pattern (6 bp):
TTTTTA
Found at i:2953946 original size:13 final size:12
Alignment explanation
Indices: 2953863--2953947 Score: 52
Period size: 13 Copynumber: 6.8 Consensus size: 12
2953853 TAGTTAATAT
2953863 TTTTTTATCTTTA
1 TTTTTTAT-TTTA
*
2953876 TTTTAT-TTTTA
1 TTTTTTATTTTA
2953887 TTTTTGT-TTTGCT-
1 TTTTT-TATTT--TA
2953900 TTTCTTTATTTTA
1 TTT-TTTATTTTA
2953913 TTTTTTTATTTTCA
1 -TTTTTTATTTT-A
*
2953927 -TTTTTATTTTG
1 TTTTTTATTTTA
2953938 TTTTATTATT
1 TTTT-TTATT
2953948 CAATTTTCTT
Statistics
Matches: 59, Mismatches: 3, Indels: 20
0.72 0.04 0.24
Matches are distributed among these distances:
11 8 0.14
12 19 0.32
13 22 0.37
14 10 0.17
ACGTcount: A:0.13, C:0.05, G:0.04, T:0.79
Consensus pattern (12 bp):
TTTTTTATTTTA
Found at i:2954062 original size:63 final size:63
Alignment explanation
Indices: 2953981--2954225 Score: 259
Period size: 63 Copynumber: 3.9 Consensus size: 63
2953971 AAAATATATA
* * *
2953981 TTTTTTGA-GAAAAGTTGAAAATATCAATTTTTCTTAAAAATAAAATTAAAAAAAAAGGGTTT
1 TTTTTTTAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAAATTAAAAAAAAAGGGTTT
** *
2954043 TTTTTTTAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAAATTTCAAAAAAAGGTTTT
1 TTTTTTTAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAAATTAAAAAAAAAGGGTTT
* * * **
2954106 TTTTTTTAGGAAAAGTTGAAAGCATAAATTTTCCTTGAAAATCAAAATTTTCAAAAAAA-----T
1 TTTTTTTAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAAT-AAAA-TTAAAAAAAAAGGGTTT
* * * * *
2954166 ATTTCTTGGGAAAAAGTTGAAAGTATCAATTTTCCTTAAAAAAAATTAATTTAAAAAAAA
1 TTTTTTTAGG-AAAAGTTGAAAGTATCAATTTTCCTTAAAAATAA--AATTAAAAAAAAA
2954226 TTAATTTTTG
Statistics
Matches: 160, Mismatches: 17, Indels: 13
0.84 0.09 0.07
Matches are distributed among these distances:
60 10 0.06
61 38 0.24
62 9 0.06
63 88 0.55
64 4 0.03
65 11 0.07
ACGTcount: A:0.47, C:0.06, G:0.11, T:0.37
Consensus pattern (63 bp):
TTTTTTTAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAAATTAAAAAAAAAGGGTTT
Found at i:2954221 original size:15 final size:15
Alignment explanation
Indices: 2954201--2954232 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
2954191 TCAATTTTCC
2954201 TTAAAAAAAATTAAT
1 TTAAAAAAAATTAAT
2954216 TTAAAAAAAATTAAT
1 TTAAAAAAAATTAAT
2954231 TT
1 TT
2954233 TTGGAGAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (15 bp):
TTAAAAAAAATTAAT
Found at i:2954255 original size:62 final size:59
Alignment explanation
Indices: 2953947--2954260 Score: 258
Period size: 63 Copynumber: 5.1 Consensus size: 59
2953937 GTTTTATTAT
* * * *
2953947 TCAATTTT-CTTTAAATAAAAA--TAAAAAATATATATTTTTTGAGAAAAGTTGAAAATA
1 TCAATTTTCCTTAAAAAAAAAATTTAAAAAAAAT-TATTTTTTGAGAAAAGTTGAAAGTA
* * * * *
2954004 TCAATTTTTCTTAAAAATAAAATTAAAAAAAAAGGGTTTTTTTTTTAGGAAAAGTTGAAAGTA
1 TCAATTTTCCTTAAAAAAAAAATTTAAAAAAAA---TTATTTTTTGA-GAAAAGTTGAAAGTA
* * * * *
2954067 TCAATTTTCCTTAAAAATAAAATTTCAAAAAAAGGTTTTTTTTTTTAGGAAAAGTTGAAAGCA
1 TCAATTTTCCTTAAAAAAAAAATTT-AAAAAAA--ATTATTTTTTGA-GAAAAGTTGAAAGTA
* * * * * *
2954130 TAAATTTTCCTTGAAAATCAAAATTTTCAAAAAAA-TATTTCTTGGGAAAAAGTTGAAAGTA
1 TCAATTTTCCTT-AAAA-AAAAAATTTAAAAAAAATTATTTTTTGAG-AAAAGTTGAAAGTA
* * *
2954191 TCAATTTTCCTTAAAAAAAATTAATTTAAAAAAAATTAATTTTTGGAGAAAAGTTCAAAATA
1 TCAATTTTCCTTAAAAAAAA--AATTTAAAAAAAATT-ATTTTTTGAGAAAAGTTGAAAGTA
2954253 TCAATTTT
1 TCAATTTT
2954261 TCCTGCACAA
Statistics
Matches: 208, Mismatches: 32, Indels: 29
0.77 0.12 0.11
Matches are distributed among these distances:
57 8 0.04
58 10 0.05
59 3 0.01
60 12 0.06
61 41 0.20
62 29 0.14
63 82 0.39
64 17 0.08
65 6 0.03
ACGTcount: A:0.47, C:0.06, G:0.10, T:0.38
Consensus pattern (59 bp):
TCAATTTTCCTTAAAAAAAAAATTTAAAAAAAATTATTTTTTGAGAAAAGTTGAAAGTA
Found at i:2968797 original size:8 final size:8
Alignment explanation
Indices: 2968784--2968832 Score: 55
Period size: 8 Copynumber: 6.0 Consensus size: 8
2968774 CTAAAATATG
2968784 ATATAAAT
1 ATATAAAT
2968792 ATATAAAT
1 ATATAAAT
*
2968800 -TATCAAT
1 ATATAAAT
*
2968807 ATATTATATT
1 ATA-TA-AAT
2968817 ATATAAAT
1 ATATAAAT
2968825 ATATAAAT
1 ATATAAAT
2968833 TATTATGTCT
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
7 6 0.18
8 20 0.59
9 3 0.09
10 5 0.15
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (8 bp):
ATATAAAT
Found at i:2968824 original size:25 final size:25
Alignment explanation
Indices: 2968791--2968838 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
2968781 ATGATATAAA
*
2968791 TATATAAAT-TATCAATATATTATAT
1 TATATAAATATATAAAT-TATTATAT
2968816 TATATAAATATATAAATTATTAT
1 TATATAAATATATAAATTATTAT
2968839 GTCTAACGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 15 0.71
26 6 0.29
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (25 bp):
TATATAAATATATAAATTATTATAT
Found at i:2975877 original size:30 final size:30
Alignment explanation
Indices: 2975843--2975902 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
2975833 CACCAAGGTG
2975843 TTATTTAGTTACATACATTTATTCAGTACA
1 TTATTTAGTTACATACATTTATTCAGTACA
2975873 TTATTTAGTTACATACATTTATTCAGTACA
1 TTATTTAGTTACATACATTTATTCAGTACA
2975903 CTAAGGCAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.33, C:0.13, G:0.07, T:0.47
Consensus pattern (30 bp):
TTATTTAGTTACATACATTTATTCAGTACA
Found at i:2975889 original size:17 final size:17
Alignment explanation
Indices: 2975843--2975891 Score: 54
Period size: 17 Copynumber: 3.1 Consensus size: 17
2975833 CACCAAGGTG
2975843 TTATTTAGTTACATAC-
1 TTATTTAGTTACATACA
2975859 --ATTTA-TT-CAGTACA
1 TTATTTAGTTACA-TACA
2975873 TTATTTAGTTACATACA
1 TTATTTAGTTACATACA
2975890 TT
1 TT
2975892 TATTCAGTAC
Statistics
Matches: 27, Mismatches: 0, Indels: 11
0.71 0.00 0.29
Matches are distributed among these distances:
12 2 0.07
13 5 0.19
14 5 0.19
16 5 0.19
17 8 0.30
18 2 0.07
ACGTcount: A:0.33, C:0.12, G:0.06, T:0.49
Consensus pattern (17 bp):
TTATTTAGTTACATACA
Found at i:2975902 original size:17 final size:17
Alignment explanation
Indices: 2975852--2975902 Score: 56
Period size: 17 Copynumber: 3.2 Consensus size: 17
2975842 GTTATTTAGT
2975852 TACATACATTTATTCAG
1 TACATACATTTATTCAG
* *
2975869 TACAT-TATTTAGT---
1 TACATACATTTATTCAG
2975882 TACATACATTTATTCAG
1 TACATACATTTATTCAG
2975899 TACA
1 TACA
2975903 CTAAGGCAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 8
0.68 0.11 0.21
Matches are distributed among these distances:
13 5 0.19
14 6 0.23
16 6 0.23
17 9 0.35
ACGTcount: A:0.35, C:0.16, G:0.06, T:0.43
Consensus pattern (17 bp):
TACATACATTTATTCAG
Found at i:2979488 original size:29 final size:29
Alignment explanation
Indices: 2979455--2979533 Score: 90
Period size: 29 Copynumber: 2.7 Consensus size: 29
2979445 ATTTAATTTG
2979455 TATTATATATATTATATTAATAAAAA-TA
1 TATTATATATATTATATTAATAAAAACTA
* *
2979483 TTATTAAATATTTTA-ATTTAATAAAAACTA
1 -TATTATATATATTATA-TTAATAAAAACTA
2979513 TATTTATATATAATTATATTA
1 TA-TTATATAT-ATTATATTA
2979534 TAATTTATAT
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
28 1 0.02
29 24 0.59
30 9 0.22
31 6 0.15
32 1 0.02
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.49
Consensus pattern (29 bp):
TATTATATATATTATATTAATAAAAACTA
Found at i:2979543 original size:12 final size:12
Alignment explanation
Indices: 2979514--2979545 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
2979504 TAAAAACTAT
2979514 ATTTATA-TATA
1 ATTTATATTATA
2979525 A-TTATATTATA
1 ATTTATATTATA
2979536 ATTTATATTA
1 ATTTATATTA
2979546 AAAATAAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
10 5 0.26
11 6 0.32
12 8 0.42
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (12 bp):
ATTTATATTATA
Found at i:2984114 original size:20 final size:20
Alignment explanation
Indices: 2984091--2984130 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
2984081 AAAAGTTAGA
2984091 AAATAATTTATTTATATTTT
1 AAATAATTTATTTATATTTT
2984111 AAATAATTTATTTATATTTT
1 AAATAATTTATTTATATTTT
2984131 TCTTGTTGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (20 bp):
AAATAATTTATTTATATTTT
Found at i:2987194 original size:64 final size:64
Alignment explanation
Indices: 2987093--2987218 Score: 243
Period size: 64 Copynumber: 2.0 Consensus size: 64
2987083 TTGCATTATA
2987093 GGCAACAAGATGCTTGGCACTTCTTGTTTACTCCATTTGTTACCATCTTGAAAGAAATTTCAGG
1 GGCAACAAGATGCTTGGCACTTCTTGTTTACTCCATTTGTTACCATCTTGAAAGAAATTTCAGG
*
2987157 GGCAACAAGATGCTTGGCACTTCTTGTTTACTTCATTTGTTACCATCTTGAAAGAAATTTCA
1 GGCAACAAGATGCTTGGCACTTCTTGTTTACTCCATTTGTTACCATCTTGAAAGAAATTTCA
2987219 CGAGTCATCC
Statistics
Matches: 61, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
64 61 1.00
ACGTcount: A:0.27, C:0.20, G:0.17, T:0.36
Consensus pattern (64 bp):
GGCAACAAGATGCTTGGCACTTCTTGTTTACTCCATTTGTTACCATCTTGAAAGAAATTTCAGG
Found at i:2994674 original size:19 final size:18
Alignment explanation
Indices: 2994647--2994700 Score: 67
Period size: 17 Copynumber: 3.1 Consensus size: 18
2994637 CTCCCTTTGG
*
2994647 TATTTTTTTTTTTACTTTT
1 TATTATTTTTTTTA-TTTT
2994666 TATTA-TTTTTTTATTTT
1 TATTATTTTTTTTATTTT
*
2994683 T-TTATTTTTATTATTTT
1 TATTATTTTTTTTATTTT
2994700 T
1 T
2994701 TATTTGTTAT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
16 3 0.09
17 17 0.53
18 8 0.25
19 4 0.12
ACGTcount: A:0.15, C:0.02, G:0.00, T:0.83
Consensus pattern (18 bp):
TATTATTTTTTTTATTTT
Found at i:2994682 original size:7 final size:7
Alignment explanation
Indices: 2994649--2994715 Score: 59
Period size: 7 Copynumber: 9.7 Consensus size: 7
2994639 CCCTTTGGTA
2994649 TTTTT-T
1 TTTTTAT
*
2994655 TTTTTAC
1 TTTTTAT
2994662 TTTTTAT
1 TTTTTAT
*
2994669 TATTT-T
1 TTTTTAT
*
2994675 TTTAT-T
1 TTTTTAT
2994681 TTTTTATT
1 TTTTTA-T
2994689 TTTATTAT
1 TTT-TTAT
2994697 TTTTTAT
1 TTTTTAT
*
2994704 TTGTTAT
1 TTTTTAT
2994711 TTTTT
1 TTTTT
2994716 GTGATCGTAC
Statistics
Matches: 49, Mismatches: 8, Indels: 7
0.77 0.12 0.11
Matches are distributed among these distances:
6 14 0.29
7 24 0.49
8 8 0.16
9 3 0.06
ACGTcount: A:0.13, C:0.01, G:0.01, T:0.84
Consensus pattern (7 bp):
TTTTTAT
Found at i:2994682 original size:24 final size:22
Alignment explanation
Indices: 2994647--2994714 Score: 84
Period size: 23 Copynumber: 2.9 Consensus size: 22
2994637 CTCCCTTTGG
2994647 TATTTTTT-TTTTTACTTTTTAT
1 TATTTTTTATTTTTA-TTTTTAT
2994669 TATTTTTTTATTTTTTTATTTTTAT
1 TA-TTTTTTA--TTTTTATTTTTAT
2994694 TATTTTTTATTTGTTATTTTT
1 TATTTTTTATTT-TTATTTTT
2994715 TGTGATCGTA
Statistics
Matches: 41, Mismatches: 0, Indels: 9
0.82 0.00 0.18
Matches are distributed among these distances:
22 5 0.12
23 14 0.34
24 7 0.17
25 9 0.22
26 6 0.15
ACGTcount: A:0.15, C:0.01, G:0.01, T:0.82
Consensus pattern (22 bp):
TATTTTTTATTTTTATTTTTAT
Found at i:2994715 original size:25 final size:23
Alignment explanation
Indices: 2994649--2994714 Score: 89
Period size: 24 Copynumber: 2.8 Consensus size: 23
2994639 CCCTTTGGTA
2994649 TTTTT-TTTTTTACTTTTTATTATT
1 TTTTTATTTTTTA-TTTTTATTA-T
2994673 TTTTTATTTTTTTATTTTTATTAT
1 TTTTTA-TTTTTTATTTTTATTAT
*
2994697 TTTTTATTTGTTATTTTT
1 TTTTTATTTTTTATTTTT
2994715 TGTGATCGTA
Statistics
Matches: 39, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
23 11 0.28
24 12 0.31
25 9 0.23
26 7 0.18
ACGTcount: A:0.14, C:0.02, G:0.02, T:0.83
Consensus pattern (23 bp):
TTTTTATTTTTTATTTTTATTAT
Found at i:2994717 original size:10 final size:9
Alignment explanation
Indices: 2994652--2994701 Score: 59
Period size: 8 Copynumber: 5.7 Consensus size: 9
2994642 TTTGGTATTT
2994652 TTTTTTTTA
1 TTTTTTTTA
*
2994661 CTTTTTATTA
1 -TTTTTTTTA
2994671 -TTTTTTTA
1 TTTTTTTTA
2994679 -TTTTTTTA
1 TTTTTTTTA
*
2994687 TTTTTATTA
1 TTTTTTTTA
2994696 TTTTTT
1 TTTTTT
2994702 ATTTGTTATT
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
8 15 0.43
9 12 0.34
10 8 0.23
ACGTcount: A:0.14, C:0.02, G:0.00, T:0.84
Consensus pattern (9 bp):
TTTTTTTTA
Found at i:2997576 original size:21 final size:20
Alignment explanation
Indices: 2997539--2997613 Score: 66
Period size: 21 Copynumber: 3.8 Consensus size: 20
2997529 AAAATATATT
2997539 AAATAT-TTTA-ATTTAATAA
1 AAATATATTTATA-TTAATAA
* *
2997558 AACTATATTTATATATAAT-T
1 AAATATATTTATAT-TAATAA
* *
2997578 AATTATATTTATATTAAAAA
1 AAATATATTTATATTAATAA
2997598 TAAATATATTTATATT
1 -AAATATATTTATATT
2997614 TATCATGTAT
Statistics
Matches: 45, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
19 8 0.18
20 18 0.40
21 19 0.42
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.49
Consensus pattern (20 bp):
AAATATATTTATATTAATAA
Found at i:3002160 original size:20 final size:20
Alignment explanation
Indices: 3002137--3002176 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
3002127 AAAAGTTAGA
3002137 AAATAATTTATTTATATTTT
1 AAATAATTTATTTATATTTT
3002157 AAATAATTTATTTATATTTT
1 AAATAATTTATTTATATTTT
3002177 TCTTGTTGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (20 bp):
AAATAATTTATTTATATTTT
Found at i:3005243 original size:64 final size:64
Alignment explanation
Indices: 3005142--3005267 Score: 243
Period size: 64 Copynumber: 2.0 Consensus size: 64
3005132 TTGCATTATA
3005142 GGCAACAAGATGCTTGGCACTTCTTGTTTACTCCATTTGTTACCATCTTGAAAGAAATTTCAGG
1 GGCAACAAGATGCTTGGCACTTCTTGTTTACTCCATTTGTTACCATCTTGAAAGAAATTTCAGG
*
3005206 GGCAACAAGATGCTTGGCACTTCTTGTTTACTTCATTTGTTACCATCTTGAAAGAAATTTCA
1 GGCAACAAGATGCTTGGCACTTCTTGTTTACTCCATTTGTTACCATCTTGAAAGAAATTTCA
3005268 CGAGTCATCC
Statistics
Matches: 61, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
64 61 1.00
ACGTcount: A:0.27, C:0.20, G:0.17, T:0.36
Consensus pattern (64 bp):
GGCAACAAGATGCTTGGCACTTCTTGTTTACTCCATTTGTTACCATCTTGAAAGAAATTTCAGG
Found at i:3012699 original size:9 final size:9
Alignment explanation
Indices: 3012680--3012721 Score: 50
Period size: 9 Copynumber: 4.6 Consensus size: 9
3012670 GGTATTTTTT
3012680 TTTTTACTT-
1 TTTTTA-TTA
*
3012689 TTTATTATTT
1 TTT-TTATTA
3012699 TTTTTATTA
1 TTTTTATTA
3012708 TTTTTATTA
1 TTTTTATTA
3012717 TTTTT
1 TTTTT
3012722 TATTTGTTAT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
9 24 0.80
10 6 0.20
ACGTcount: A:0.17, C:0.02, G:0.00, T:0.81
Consensus pattern (9 bp):
TTTTTATTA
Found at i:3012701 original size:21 final size:21
Alignment explanation
Indices: 3012672--3012722 Score: 84
Period size: 21 Copynumber: 2.4 Consensus size: 21
3012662 CTCCCTTTGG
*
3012672 TATTTTTTTTTTTACTTTTTAT
1 TATTTTTTTTATTA-TTTTTAT
3012694 TATTTTTTTTATTATTTTTAT
1 TATTTTTTTTATTATTTTTAT
3012715 TATTTTTT
1 TATTTTTT
3012723 ATTTGTTATT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
21 15 0.54
22 13 0.46
ACGTcount: A:0.16, C:0.02, G:0.00, T:0.82
Consensus pattern (21 bp):
TATTTTTTTTATTATTTTTAT
Found at i:3012702 original size:12 final size:12
Alignment explanation
Indices: 3012687--3012736 Score: 66
Period size: 12 Copynumber: 4.2 Consensus size: 12
3012677 TTTTTTTTAC
3012687 TTTTTATTATTT
1 TTTTTATTATTT
3012699 TTTTTATTATTT
1 TTTTTATTATTT
*
3012711 TTATTATT-TTT
1 TTTTTATTATTT
* *
3012722 TATTTGTTATTT
1 TTTTTATTATTT
3012734 TTT
1 TTT
3012737 GTGATCGTAC
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
11 8 0.25
12 24 0.75
ACGTcount: A:0.16, C:0.00, G:0.02, T:0.82
Consensus pattern (12 bp):
TTTTTATTATTT
Found at i:3015623 original size:2 final size:2
Alignment explanation
Indices: 3015616--3015658 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
3015606 AAAAGGTGTT
3015616 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3015658 T
1 T
3015659 TCTCTTCAAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3020417 original size:25 final size:25
Alignment explanation
Indices: 3020389--3020438 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
3020379 GAATTTTAAC
3020389 CCAAATCTTAACAAAAGCTAATGAA
1 CCAAATCTTAACAAAAGCTAATGAA
3020414 CCAAATCTTAACAAAAGCTAATGAA
1 CCAAATCTTAACAAAAGCTAATGAA
3020439 TAAGACTAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.52, C:0.20, G:0.08, T:0.20
Consensus pattern (25 bp):
CCAAATCTTAACAAAAGCTAATGAA
Found at i:3027178 original size:85 final size:84
Alignment explanation
Indices: 3026942--3027164 Score: 259
Period size: 86 Copynumber: 2.6 Consensus size: 84
3026932 GTGGCCATAA
* * * * *
3026942 AAAATATGGACCTAAAGGTGCTGATTTCAAGCCCATAAAATTGCTAAATGGACCTAAAATTGTAA
1 AAAATTTGGACCCAAAGCTGCTGATTCCAAGCCCAT-ACATTGCTAAATGGACCTAAAATTGTAA
* **
3027007 TCATTGTGGGCCAACGACCAT
65 -CATTGTCGGAAAACGACCAT
** * *
3027028 AAAATTATGGGTCCAAGGCTGCTGATTCCAA-CCCAAAGCATTGCTAAATGGACCTAAAATTGTA
1 AAAATT-TGGACCCAAAGCTGCTGATTCCAAGCCCATA-CATTGCTAAATGGACCTAAAATTGTA
*
3027092 ACATATGTCGGAAAATGACCAT
64 ACAT-TGTCGGAAAACGACCAT
* *
3027114 AAAATTTGGACCCAAAGTTGCTGATTCCAAGCCCATACACTGCTAAATGGA
1 AAAATTTGGACCCAAAGCTGCTGATTCCAAGCCCATACATTGCTAAATGGA
3027165 GCTTTACTTG
Statistics
Matches: 114, Mismatches: 19, Indels: 9
0.80 0.13 0.06
Matches are distributed among these distances:
85 37 0.32
86 59 0.52
87 18 0.16
ACGTcount: A:0.37, C:0.20, G:0.18, T:0.25
Consensus pattern (84 bp):
AAAATTTGGACCCAAAGCTGCTGATTCCAAGCCCATACATTGCTAAATGGACCTAAAATTGTAAC
ATTGTCGGAAAACGACCAT
Found at i:3027438 original size:27 final size:26
Alignment explanation
Indices: 3027394--3027468 Score: 69
Period size: 29 Copynumber: 2.7 Consensus size: 26
3027384 TTTAAGTATT
* *
3027394 ATATTAATTAATAGATTTATAATTCAA
1 ATATTAATTAA-AAATTTAAAATTCAA
3027421 ATATTACATTAAAAATTTTTAAAATTCAA
1 ATATTA-ATTAAAAA--TTTAAAATTCAA
*
3027450 ATGTTATATTAAAATATTT
1 ATATTA-ATTAAAA-ATTT
3027469 TATTATAATT
Statistics
Matches: 40, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
27 8 0.20
28 8 0.20
29 23 0.57
30 1 0.03
ACGTcount: A:0.48, C:0.04, G:0.03, T:0.45
Consensus pattern (26 bp):
ATATTAATTAAAAATTTAAAATTCAA
Found at i:3027448 original size:29 final size:30
Alignment explanation
Indices: 3027409--3027469 Score: 88
Period size: 29 Copynumber: 2.1 Consensus size: 30
3027399 AATTAATAGA
*
3027409 TTTATAATTCAAATATTACATTAAAA-ATT
1 TTTAAAATTCAAATATTACATTAAAATATT
* *
3027438 TTTAAAATTCAAATGTTATATTAAAATATT
1 TTTAAAATTCAAATATTACATTAAAATATT
3027468 TT
1 TT
3027470 ATTATAATTT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
29 23 0.82
30 5 0.18
ACGTcount: A:0.46, C:0.05, G:0.02, T:0.48
Consensus pattern (30 bp):
TTTAAAATTCAAATATTACATTAAAATATT
Found at i:3031223 original size:2 final size:2
Alignment explanation
Indices: 3031216--3031248 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
3031206 TCCCTTTAAT
3031216 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
3031249 TATGCAAAGG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:3033909 original size:17 final size:17
Alignment explanation
Indices: 3033883--3033915 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
3033873 CTTGCAAGCA
3033883 TTATCCTTCTATATATC
1 TTATCCTTCTATATATC
*
3033900 TTATCTTTCTATATAT
1 TTATCCTTCTATATAT
3033916 GCCTTTTAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.24, C:0.18, G:0.00, T:0.58
Consensus pattern (17 bp):
TTATCCTTCTATATATC
Found at i:3035511 original size:18 final size:18
Alignment explanation
Indices: 3035468--3035526 Score: 52
Period size: 16 Copynumber: 3.3 Consensus size: 18
3035458 AAAAAAAAAC
*
3035468 TTTTCGTGTATAACTATT
1 TTTTCGTATATAACTATT
3035486 TTTT--TATATAA-TATAT
1 TTTTCGTATATAACTAT-T
*
3035502 TTTTCGTATATTATCTATT
1 TTTTCGTATA-TAACTATT
3035521 TATTTC
1 T-TTTC
3035527 AATAAAAATA
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
15 3 0.09
16 11 0.33
18 8 0.24
19 4 0.12
20 7 0.21
ACGTcount: A:0.25, C:0.08, G:0.05, T:0.61
Consensus pattern (18 bp):
TTTTCGTATATAACTATT
Found at i:3049645 original size:2 final size:2
Alignment explanation
Indices: 3049638--3049672 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
3049628 GTGTATCCAC
3049638 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3049673 TATGAATTAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3056336 original size:2 final size:2
Alignment explanation
Indices: 3056329--3056356 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3056319 AACTATGAAG
3056329 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3056357 CTTCGCCCAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3062656 original size:17 final size:17
Alignment explanation
Indices: 3062634--3062667 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
3062624 CCATGCGCCA
3062634 CTTTTTGTT-ATTTTTTT
1 CTTTTT-TTAATTTTTTT
3062651 CTTTTTTTAATTTTTTT
1 CTTTTTTTAATTTTTTT
3062668 AATTGTACCT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 2 0.12
17 14 0.88
ACGTcount: A:0.09, C:0.06, G:0.03, T:0.82
Consensus pattern (17 bp):
CTTTTTTTAATTTTTTT
Found at i:3065873 original size:13 final size:13
Alignment explanation
Indices: 3065838--3065875 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
3065828 TTAAACTTAA
3065838 TTTTAATTTTTAT
1 TTTTAATTTTTAT
* *
3065851 ATATAATTTTTAT
1 TTTTAATTTTTAT
3065864 TTTT-ATTTTTAT
1 TTTTAATTTTTAT
3065876 GTGAATTAAA
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
12 8 0.38
13 13 0.62
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (13 bp):
TTTTAATTTTTAT
Found at i:3068161 original size:14 final size:14
Alignment explanation
Indices: 3068142--3068178 Score: 74
Period size: 14 Copynumber: 2.6 Consensus size: 14
3068132 ACCAAGGAAG
3068142 AAATTTATTGTTAT
1 AAATTTATTGTTAT
3068156 AAATTTATTGTTAT
1 AAATTTATTGTTAT
3068170 AAATTTATT
1 AAATTTATT
3068179 TTTTTGAATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.57
Consensus pattern (14 bp):
AAATTTATTGTTAT
Found at i:3069031 original size:17 final size:16
Alignment explanation
Indices: 3068992--3069034 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
3068982 TTTAGATGAA
3068992 TAAATTAAATAATAAC
1 TAAATTAAATAATAAC
** *
3069008 TTTATTAATATAATATC
1 TAAATTAA-ATAATAAC
3069025 TAAATTAAAT
1 TAAATTAAAT
3069035 TAAATAAATA
Statistics
Matches: 21, Mismatches: 5, Indels: 2
0.75 0.18 0.07
Matches are distributed among these distances:
16 8 0.38
17 13 0.62
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (16 bp):
TAAATTAAATAATAAC
Found at i:3069258 original size:12 final size:12
Alignment explanation
Indices: 3069241--3069265 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3069231 TGTTGACTCC
3069241 ATTTATTATAAA
1 ATTTATTATAAA
3069253 ATTTATTATAAA
1 ATTTATTATAAA
3069265 A
1 A
3069266 GCTAGATGCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (12 bp):
ATTTATTATAAA
Found at i:3069775 original size:18 final size:18
Alignment explanation
Indices: 3069724--3069777 Score: 54
Period size: 18 Copynumber: 2.9 Consensus size: 18
3069714 ATTTATCTTT
* *
3069724 TTAAATATAATTAAAAAA
1 TTAAAAATAATAAAAAAA
*
3069742 TTAAAAATAACAAAAAAAA
1 TTAAAAATAA-TAAAAAAA
**
3069761 TTAAAGCTAATAAAAAA
1 TTAAAAATAATAAAAAA
3069778 CAAAGCCCAC
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
18 15 0.52
19 14 0.48
ACGTcount: A:0.70, C:0.04, G:0.02, T:0.24
Consensus pattern (18 bp):
TTAAAAATAATAAAAAAA
Found at i:3071269 original size:22 final size:24
Alignment explanation
Indices: 3071244--3071287 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
3071234 TATTTTTTAA
3071244 TATAAAT-T-ATATTTTAATTATG
1 TATAAATATAATATTTTAATTATG
*
3071266 TATAAATATAATATTTTTATTA
1 TATAAATATAATATTTTAATTA
3071288 AATTAAGGTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 7 0.37
23 1 0.05
24 11 0.58
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (24 bp):
TATAAATATAATATTTTAATTATG
Found at i:3072268 original size:7 final size:7
Alignment explanation
Indices: 3072226--3072264 Score: 62
Period size: 7 Copynumber: 5.7 Consensus size: 7
3072216 AAAAAAAAGT
3072226 AAAAAT-
1 AAAAATA
3072232 AAAAATA
1 AAAAATA
3072239 AAAAATA
1 AAAAATA
3072246 AAAAATA
1 AAAAATA
*
3072253 AAAAACA
1 AAAAATA
3072260 AAAAA
1 AAAAA
3072265 CAAATAAGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
6 6 0.19
7 25 0.81
ACGTcount: A:0.87, C:0.03, G:0.00, T:0.10
Consensus pattern (7 bp):
AAAAATA
Found at i:3073100 original size:16 final size:16
Alignment explanation
Indices: 3073079--3073113 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
3073069 CAAACCTTTG
3073079 ATATCAAGTGAATTTC
1 ATATCAAGTGAATTTC
3073095 ATATCAAGTGAATTTC
1 ATATCAAGTGAATTTC
3073111 ATA
1 ATA
3073114 CAAAAAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.40, C:0.11, G:0.11, T:0.37
Consensus pattern (16 bp):
ATATCAAGTGAATTTC
Found at i:3073294 original size:17 final size:18
Alignment explanation
Indices: 3073264--3073306 Score: 70
Period size: 17 Copynumber: 2.4 Consensus size: 18
3073254 TTAAAAAAGC
*
3073264 AATAAAAAGTTTTTAAAA
1 AATAAAAAGATTTTAAAA
3073282 AATAAAAA-ATTTTAAAA
1 AATAAAAAGATTTTAAAA
3073299 AATAAAAA
1 AATAAAAA
3073307 TAATTGAAGA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 16 0.67
18 8 0.33
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (18 bp):
AATAAAAAGATTTTAAAA
Found at i:3079358 original size:16 final size:16
Alignment explanation
Indices: 3079337--3079376 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
3079327 AATCTTTAAA
*
3079337 ATCATCGTAAATCATT
1 ATCATCATAAATCATT
3079353 ATCATCATAAATCATT
1 ATCATCATAAATCATT
*
3079369 ATAATCAT
1 ATCATCAT
3079377 TATTATCATA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.42, C:0.17, G:0.03, T:0.38
Consensus pattern (16 bp):
ATCATCATAAATCATT
Found at i:3079377 original size:25 final size:25
Alignment explanation
Indices: 3079346--3079395 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
3079336 AATCATCGTA
3079346 AATCATTATCATCATAAATCATTAT
1 AATCATTATCATCATAAATCATTAT
*
3079371 AATCATTATTATCATAAATCATTAT
1 AATCATTATCATCATAAATCATTAT
3079396 TATTATTCAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.44, C:0.14, G:0.00, T:0.42
Consensus pattern (25 bp):
AATCATTATCATCATAAATCATTAT
Found at i:3085504 original size:53 final size:52
Alignment explanation
Indices: 3085421--3085523 Score: 179
Period size: 53 Copynumber: 2.0 Consensus size: 52
3085411 ATTAGGAGCA
3085421 TTTTCAATATTAATTTGCTCATCTCGAACATTGGTGATTTCAGATTCATCCT
1 TTTTCAATATTAATTTGCTCATCTCGAACATTGGTGATTTCAGATTCATCCT
* *
3085473 TTTTCCAATATTAATTTGCTCATCTCTAACATTGGTGATTTCATATTCATC
1 TTTT-CAATATTAATTTGCTCATCTCGAACATTGGTGATTTCAGATTCATC
3085524 TCTTCTCTTA
Statistics
Matches: 48, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
52 4 0.08
53 44 0.92
ACGTcount: A:0.25, C:0.19, G:0.10, T:0.46
Consensus pattern (52 bp):
TTTTCAATATTAATTTGCTCATCTCGAACATTGGTGATTTCAGATTCATCCT
Found at i:3086301 original size:16 final size:16
Alignment explanation
Indices: 3086282--3086312 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
3086272 AATCTTTAAA
3086282 ATCATCATAAATCATT
1 ATCATCATAAATCATT
3086298 ATCATCATAAATCAT
1 ATCATCATAAATCAT
3086313 CATTATTATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.45, C:0.19, G:0.00, T:0.35
Consensus pattern (16 bp):
ATCATCATAAATCATT
Found at i:3086653 original size:15 final size:15
Alignment explanation
Indices: 3086633--3086668 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
3086623 TTATATAGAG
3086633 AAATGCAAAATAATT
1 AAATGCAAAATAATT
3086648 AAATGCAAAATAATT
1 AAATGCAAAATAATT
*
3086663 ATATGC
1 AAATGC
3086669 TTGATTCTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.56, C:0.08, G:0.08, T:0.28
Consensus pattern (15 bp):
AAATGCAAAATAATT
Found at i:3095295 original size:3 final size:3
Alignment explanation
Indices: 3095287--3095311 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
3095277 AAGGACTGAG
3095287 TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA T
3095312 GGAAGCTAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:3102661 original size:22 final size:22
Alignment explanation
Indices: 3102636--3102876 Score: 126
Period size: 22 Copynumber: 10.9 Consensus size: 22
3102626 ATGATTAGTA
* * *
3102636 ATTAAGTTATTATTAATTTATT
1 ATTAAGTTATTAATGATTTACT
* * ***
3102658 ATTATGTTATCAGCAATTTACT
1 ATTAAGTTATTAATGATTTACT
* * *
3102680 ATTAAGTTATCAATGATATATT
1 ATTAAGTTATTAATGATTTACT
* *
3102702 ACTAAATTATTAATGATTTACT
1 ATTAAGTTATTAATGATTTACT
* * ** * *
3102724 ATTAAATCAGCATTGATTTATT
1 ATTAAGTTATTAATGATTTACT
* * *
3102746 ATTAATTTATGAATGATTTATT
1 ATTAAGTTATTAATGATTTACT
* *
3102768 ACTAAGTTATAAATGATTTACT
1 ATTAAGTTATTAATGATTTACT
* * * *
3102790 CTTAAATTGTTAATAATTTACT
1 ATTAAGTTATTAATGATTTACT
* * **
3102812 ATCAAGTTATTGATGATTTGTT
1 ATTAAGTTATTAATGATTTACT
*
3102834 AATAAAGTTA-TAACTGATTTACT
1 -ATTAAGTTATTAA-TGATTTACT
* *
3102857 TTTAATTTA-TAGATGATTTA
1 ATTAAGTTATTA-ATGATTTA
3102877 TTACAATACT
Statistics
Matches: 164, Mismatches: 52, Indels: 6
0.74 0.23 0.03
Matches are distributed among these distances:
22 148 0.90
23 16 0.10
ACGTcount: A:0.37, C:0.06, G:0.09, T:0.48
Consensus pattern (22 bp):
ATTAAGTTATTAATGATTTACT
Found at i:3102721 original size:44 final size:44
Alignment explanation
Indices: 3102673--3103136 Score: 197
Period size: 44 Copynumber: 10.4 Consensus size: 44
3102663 GTTATCAGCA
*
3102673 ATTTACTATTAAGTTATCAATGATATATTACTAAATTATTAATG
1 ATTTACTATTAAGTTATCAATGATTTATTACTAAATTATTAATG
* * * * * * *
3102717 ATTTACTATTAAATCAGCATTGATTTATTATTAATTTATGAATG
1 ATTTACTATTAAGTTATCAATGATTTATTACTAAATTATTAATG
* * * * * *
3102761 ATTTATTACTAAGTTATAAATGATTTACT-CTTAAATTGTTAATA
1 ATTTACTATTAAGTTATCAATGATTTATTAC-TAAATTATTAATG
* ** * *
3102805 ATTTACTATCAAGTTATTGATGATTTGTTAATAAAGTTA-TAACTG
1 ATTTACTATTAAGTTATCAATGATTTATTACTAAA-TTATTAA-TG
* * * *
3102850 ATTTACTTTTAATTTAT-AGATGATTTATTACAATACTATCAATGATTAACTA
1 ATTTACTATTAAGTTATCA-ATGATTTA-T----TACTA--AATTATTAA-TG
* * * * * * *
3102902 AGTTACTATTAAATTATCACTAATTTATTATTAAATTATCAATA
1 ATTTACTATTAAGTTATCAATGATTTATTACTAAATTATTAATG
* * * * **
3102946 ATTTAC-ATATAAATTATTAATGATTTACTATTATGTTATT-ATG
1 ATTTACTAT-TAAGTTATCAATGATTTATTACTAAATTATTAATG
* * * * * * * *
3102989 CATTTACTATTATGTTATCATTCATTTACTACTTAGTTTTTAATT
1 -ATTTACTATTAAGTTATCAATGATTTATTACTAAATTATTAATG
* * * * * * **
3103034 ATTTACTATAAAATCATTACAT-ATTTATTACTAAATGAATCGTG
1 ATTTACTATTAAGTTATCA-ATGATTTATTACTAAATTATTAATG
* * * * * * *
3103078 ATTCATTATTAAGCTATCATTAATTTA-TACTAAATTA-CAATA
1 ATTTACTATTAAGTTATCAATGATTTATTACTAAATTATTAATG
*
3103120 ATTTAGTATTAAGTTAT
1 ATTTACTATTAAGTTAT
3103137 TTAAATATTA
Statistics
Matches: 303, Mismatches: 97, Indels: 42
0.69 0.22 0.10
Matches are distributed among these distances:
42 15 0.05
43 14 0.05
44 198 0.65
45 36 0.12
46 1 0.00
47 4 0.01
50 4 0.01
51 3 0.01
52 27 0.09
53 1 0.00
ACGTcount: A:0.38, C:0.08, G:0.07, T:0.47
Consensus pattern (44 bp):
ATTTACTATTAAGTTATCAATGATTTATTACTAAATTATTAATG
Found at i:3102727 original size:66 final size:63
Alignment explanation
Indices: 3102620--3102796 Score: 167
Period size: 66 Copynumber: 2.7 Consensus size: 63
3102610 TATAAAAAAA
* * * * * *
3102620 TTATCAATGATTAGTAATTAAGTTATTATTAATTTATTATTATGTTATCAGCA-ATTTACTATTA
1 TTATCAATGATTA-TTACTAAGTTATTAATGATTTACTATTA---AATCAGCATATTTACTATTA
3102684 AG
62 AG
* *
3102686 TTATCAATGATATATTACTAAATTATTAATGATTTACTATTAAATCAGCATTGATTTATTATTAA
1 TTATCAATGAT-TATTACTAAGTTATTAATGATTTACTATTAAATCAGCA-T-ATTTACTATTAA
*
3102751 T
63 G
* * *
3102752 TTATGAATGATTTATTACTAAGTTATAAATGATTTACTCTTAAAT
1 TTATCAATGA-TTATTACTAAGTTATTAATGATTTACTATTAAAT
3102797 TGTTAATAAT
Statistics
Matches: 93, Mismatches: 13, Indels: 10
0.80 0.11 0.09
Matches are distributed among these distances:
63 7 0.08
66 83 0.89
67 3 0.03
ACGTcount: A:0.38, C:0.07, G:0.08, T:0.47
Consensus pattern (63 bp):
TTATCAATGATTATTACTAAGTTATTAATGATTTACTATTAAATCAGCATATTTACTATTAAG
Found at i:3102809 original size:66 final size:66
Alignment explanation
Indices: 3102672--3102861 Score: 195
Period size: 66 Copynumber: 2.9 Consensus size: 66
3102662 TGTTATCAGC
* * * * *
3102672 AATTTACTATTAAGTTATCAATGATATATTACTAAATTATTAATGATTTACTATTAAATCAGCAT
1 AATTTACTATTAAGTTATGAATGATTTATTACTAAGTTATAAATGATTTACTATTAAATCAGCAA
3102737 T
66 T
* * * * * *
3102738 GATTTATTATTAATTTATGAATGATTTATTACTAAGTTATAAATGATTTACTCTTAAAT-TGTTA
1 AATTTACTATTAAGTTATGAATGATTTATTACTAAGTTATAAATGATTTACTATTAAATCAG-CA
3102802 AT
65 AT
* * * * *
3102804 AATTTACTATCAAGTTATTG-ATGATTTGTTAATAAAGTTATAACTGATTTACTTTTAA
1 AATTTACTATTAAGTTA-TGAATGATTTATTACT-AAGTTATAAATGATTTACTATTAA
3102862 TTTATAGATG
Statistics
Matches: 102, Mismatches: 19, Indels: 5
0.81 0.15 0.04
Matches are distributed among these distances:
65 1 0.01
66 77 0.75
67 24 0.24
ACGTcount: A:0.38, C:0.07, G:0.08, T:0.47
Consensus pattern (66 bp):
AATTTACTATTAAGTTATGAATGATTTATTACTAAGTTATAAATGATTTACTATTAAATCAGCAA
T
Found at i:3102923 original size:22 final size:22
Alignment explanation
Indices: 3102898--3102978 Score: 92
Period size: 22 Copynumber: 3.7 Consensus size: 22
3102888 TCAATGATTA
*
3102898 ACTAAGTTACTATTAAATTATC
1 ACTAATTTACTATTAAATTATC
*
3102920 ACTAATTTATTATTAAATTATC
1 ACTAATTTACTATTAAATTATC
* *
3102942 AATAATTTAC-ATATAAATTATT
1 ACTAATTTACTAT-TAAATTATC
* *
3102964 AATGATTTACTATTA
1 ACTAATTTACTATTA
3102979 TGTTATTATG
Statistics
Matches: 51, Mismatches: 6, Indels: 4
0.84 0.10 0.07
Matches are distributed among these distances:
21 2 0.04
22 47 0.92
23 2 0.04
ACGTcount: A:0.43, C:0.09, G:0.02, T:0.46
Consensus pattern (22 bp):
ACTAATTTACTATTAAATTATC
Found at i:3102984 original size:22 final size:22
Alignment explanation
Indices: 3102959--3103042 Score: 91
Period size: 22 Copynumber: 3.8 Consensus size: 22
3102949 TACATATAAA
3102959 TTATTAATGATTTACTATTATG
1 TTATTAATGATTTACTATTATG
3102981 TTATT-ATGCATTTACTATTATG
1 TTATTAATG-ATTTACTATTATG
* * *
3103003 TTATCATTCATTTACTACTTA-G
1 TTATTAATGATTTACTA-TTATG
* *
3103025 TTTTTAATTATTTACTAT
1 TTATTAATGATTTACTAT
3103043 AAAATCATTA
Statistics
Matches: 52, Mismatches: 7, Indels: 7
0.79 0.11 0.11
Matches are distributed among these distances:
21 4 0.08
22 44 0.85
23 4 0.08
ACGTcount: A:0.29, C:0.10, G:0.06, T:0.56
Consensus pattern (22 bp):
TTATTAATGATTTACTATTATG
Found at i:3103172 original size:25 final size:24
Alignment explanation
Indices: 3103142--3103235 Score: 67
Period size: 21 Copynumber: 4.1 Consensus size: 24
3103132 GTTATTTAAA
*
3103142 TATTAAGTTATTAATAATTTACTAC
1 TATTAAATTA-TAATAATTTACTAC
*
3103167 TATTAAATTATATTAATTTACT--
1 TATTAAATTATAATAATTTACTAC
*
3103189 T-TTAAATT-TCAATAA-TTA--AT
1 TATTAAATTAT-AATAATTTACTAC
* *
3103209 TATTAAATTATCATTGATTTACTAC
1 TATTAAATTAT-AATAATTTACTAC
3103234 TA
1 TA
3103236 AATTACCTAT
Statistics
Matches: 55, Mismatches: 6, Indels: 16
0.71 0.08 0.21
Matches are distributed among these distances:
20 5 0.09
21 18 0.33
22 6 0.11
23 3 0.05
24 11 0.20
25 12 0.22
ACGTcount: A:0.40, C:0.07, G:0.02, T:0.50
Consensus pattern (24 bp):
TATTAAATTATAATAATTTACTAC
Found at i:3103240 original size:22 final size:22
Alignment explanation
Indices: 3103164--3103384 Score: 128
Period size: 22 Copynumber: 10.0 Consensus size: 22
3103154 AATAATTTAC
3103164 TACTATTAAATTAT-ATTAATT
1 TACTATTAAATTATCATTAATT
* *
3103185 TACTTTTAAATT-TCAATAATT
1 TACTATTAAATTATCATTAATT
* * *
3103206 AATTATTAAATTATCATTGATT
1 TACTATTAAATTATCATTAATT
* * *
3103228 TACTACTAAATTA-CCTATACTT
1 TACTATTAAATTATCAT-TAATT
*
3103250 TACTATTAAGTTTATCAATTAA-T
1 TACTATTAA-ATTATC-ATTAATT
** * * * *
3103273 TACTCCTAAACTGA-AATTGATC
1 TACTATTAAA-TTATCATTAATT
*
3103295 TACTATTAAGTTATCATTAATT
1 TACTATTAAATTATCATTAATT
* *
3103317 TACCATTAAATTATCATTGATT
1 TACTATTAAATTATCATTAATT
* * * **
3103339 AACAACTAAATTATCACTTTTTT
1 TACTATTAAATTATCA-TTAATT
** *
3103362 TTGTATTAACTTATCATTAATT
1 TACTATTAAATTATCATTAATT
3103384 T
1 T
3103385 CCTAATATGT
Statistics
Matches: 143, Mismatches: 47, Indels: 19
0.68 0.22 0.09
Matches are distributed among these distances:
20 1 0.01
21 34 0.24
22 77 0.54
23 27 0.19
24 3 0.02
25 1 0.01
ACGTcount: A:0.38, C:0.12, G:0.03, T:0.47
Consensus pattern (22 bp):
TACTATTAAATTATCATTAATT
Found at i:3103913 original size:317 final size:318
Alignment explanation
Indices: 3103337--3103974 Score: 1206
Period size: 317 Copynumber: 2.0 Consensus size: 318
3103327 TTATCATTGA
3103337 TTAACAACTAAATTATCACTTTTTTTTGTATTAACTTATCATTAATTTCCTAATATGTTATTATG
1 TTAACAACTAAATTATCACTTTTTTTTGTATTAACTTATCATTAATTTCCTAATATGTTATTATG
3103402 CATTCAAAACTATGAAATATGGAATTAAAAAAGTTCACTAATAATATACGAGATAATTTTCTTTT
66 CATTCAAAACTATGAAATATGGAATTAAAAAAGTTCACTAATAATATACGAGATAATTTTCTTTT
*
3103467 TGTATAATAACATTATTATTTTATTTAAGTTTAGAATTTTTTTCATGAATTCTTTTTATTGAATA
131 TGTATAATAACATTATTATTTTATTTAAGTTTAGAATTTTTTTCATGAATTCTTTTTATTAAATA
*
3103532 GGTTCATGATAGTTTTATCCTAGTCCTTAAAATGAAAGTTTTAACTTCATTTCTATTAGTAATCA
196 GGTTCATGATAGTTTTATCCTAGTCCTTAAAATGAAAGTTTTAACTTCATTTCTACTAGTAATCA
* *
3103597 AAGTTCAATTCCTATAAACTTTAAGTATAAAAAAAGTTATTAATGATTAACTATTAAG
261 AAGTTCAATTCCTATAAACTTCAAGTATAAAAAAAGTTATTAATAATTAACTATTAAG
3103655 TTAACAACTAAATTATCACTTTTTTTTGTATTAACTTATCATTAATTTCCTAATATGTTATTATG
1 TTAACAACTAAATTATCACTTTTTTTTGTATTAACTTATCATTAATTTCCTAATATGTTATTATG
*
3103720 CATTTAAAACTATGAAATATGGAATTAAAAAAGTTCACTAATAATATACGAGATAATTTT-TTTT
66 CATTCAAAACTATGAAATATGGAATTAAAAAAGTTCACTAATAATATACGAGATAATTTTCTTTT
3103784 TGTATAATAACATTATTATTTTATTTAAGTTTAGAATTTTTTTCATGAATTCTTTTTATTAAATA
131 TGTATAATAACATTATTATTTTATTTAAGTTTAGAATTTTTTTCATGAATTCTTTTTATTAAATA
3103849 GGTTCATGATAGTTTTATCCTAGTCCTTAAAATGAAAGTTTTAACTTCATTTCTACTAGTAATCA
196 GGTTCATGATAGTTTTATCCTAGTCCTTAAAATGAAAGTTTTAACTTCATTTCTACTAGTAATCA
* *
3103914 AAGTTCAATTCTTATCAACTTCAAGTATAAAAAAAGTTATTAATAATTAACTATTAAG
261 AAGTTCAATTCCTATAAACTTCAAGTATAAAAAAAGTTATTAATAATTAACTATTAAG
3103972 TTA
1 TTA
3103975 TCAGTTATTT
Statistics
Matches: 313, Mismatches: 7, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
317 189 0.60
318 124 0.40
ACGTcount: A:0.37, C:0.10, G:0.08, T:0.45
Consensus pattern (318 bp):
TTAACAACTAAATTATCACTTTTTTTTGTATTAACTTATCATTAATTTCCTAATATGTTATTATG
CATTCAAAACTATGAAATATGGAATTAAAAAAGTTCACTAATAATATACGAGATAATTTTCTTTT
TGTATAATAACATTATTATTTTATTTAAGTTTAGAATTTTTTTCATGAATTCTTTTTATTAAATA
GGTTCATGATAGTTTTATCCTAGTCCTTAAAATGAAAGTTTTAACTTCATTTCTACTAGTAATCA
AAGTTCAATTCCTATAAACTTCAAGTATAAAAAAAGTTATTAATAATTAACTATTAAG
Found at i:3104028 original size:22 final size:22
Alignment explanation
Indices: 3103947--3104072 Score: 83
Period size: 22 Copynumber: 5.7 Consensus size: 22
3103937 AGTATAAAAA
* * *
3103947 AAGTTATTAATAATTAACTATT
1 AAGTTATCAATTATTTACTATT
* **
3103969 AAGTTATCAGTTATTTACTGCT
1 AAGTTATCAATTATTTACTATT
** *
3103991 AAGTTATCAAAAATTTAGTATT
1 AAGTTATCAATTATTTACTATT
* *
3104013 AAATTATCAATTATTTACTTTT
1 AAGTTATCAATTATTTACTATT
* * * *
3104035 AATTTATGAATAATTT-GTCATT
1 AAGTTATCAATTATTTACT-ATT
* *
3104057 AAGTTATGAATGATTT
1 AAGTTATCAATTATTT
3104073 CTTTTTTAAA
Statistics
Matches: 79, Mismatches: 24, Indels: 2
0.75 0.23 0.02
Matches are distributed among these distances:
21 1 0.01
22 78 0.99
ACGTcount: A:0.38, C:0.06, G:0.09, T:0.47
Consensus pattern (22 bp):
AAGTTATCAATTATTTACTATT
Found at i:3104050 original size:44 final size:44
Alignment explanation
Indices: 3103947--3104077 Score: 131
Period size: 44 Copynumber: 3.0 Consensus size: 44
3103937 AGTATAAAAA
* * * * **
3103947 AAGTTATTAATAATTAACTATTAAGTTATCAGTTATTTACTGCT
1 AAGTTATCAATAATTTAGTATTAAGTTATCAATTATTTACTTTT
* *
3103991 AAGTTATCAAAAATTTAGTATTAAATTATCAATTATTTACTTTT
1 AAGTTATCAATAATTTAGTATTAAGTTATCAATTATTTACTTTT
* * * *
3104035 AATTTATGAATAATTT-GTCATTAAGTTATGAATGATTT-CTTTT
1 AAGTTATCAATAATTTAGT-ATTAAGTTATCAATTATTTACTTTT
3104078 TTAAATTGTT
Statistics
Matches: 72, Mismatches: 14, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
43 7 0.10
44 65 0.90
ACGTcount: A:0.37, C:0.07, G:0.08, T:0.48
Consensus pattern (44 bp):
AAGTTATCAATAATTTAGTATTAAGTTATCAATTATTTACTTTT
Found at i:3104333 original size:19 final size:19
Alignment explanation
Indices: 3104269--3104335 Score: 59
Period size: 19 Copynumber: 3.6 Consensus size: 19
3104259 TTGCTAAGTT
*
3104269 ATTAATTTACTAGGTTATC
1 ATTAATTTATTAGGTTATC
* * *
3104288 ATTTATTTAATA--TTATAT
1 ATTAATTTATTAGGTTAT-C
*
3104306 ATTTA-TTATTAGGTTATC
1 ATTAATTTATTAGGTTATC
3104324 ATTAATTTATTA
1 ATTAATTTATTA
3104336 CTTAATTTTT
Statistics
Matches: 38, Mismatches: 6, Indels: 8
0.73 0.12 0.15
Matches are distributed among these distances:
17 9 0.24
18 9 0.24
19 20 0.53
ACGTcount: A:0.34, C:0.04, G:0.06, T:0.55
Consensus pattern (19 bp):
ATTAATTTATTAGGTTATC
Found at i:3104449 original size:22 final size:21
Alignment explanation
Indices: 3104401--3104465 Score: 60
Period size: 22 Copynumber: 3.0 Consensus size: 21
3104391 TCAAGTAATT
*
3104401 ATTGATTTATATTAAATTAT-
1 ATTGATTTATATTAAGTTATA
*
3104421 GTATGATTTATTATTAAGTTATA
1 AT-TGATTTA-TATTAAGTTATA
* *
3104444 ATTGATTAACTATTATGTTATA
1 ATTGATTTA-TATTAAGTTATA
3104466 GATGATTCAC
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
20 1 0.03
21 7 0.19
22 27 0.75
23 1 0.03
ACGTcount: A:0.37, C:0.02, G:0.09, T:0.52
Consensus pattern (21 bp):
ATTGATTTATATTAAGTTATA
Found at i:3104471 original size:22 final size:21
Alignment explanation
Indices: 3104423--3104519 Score: 59
Period size: 22 Copynumber: 4.4 Consensus size: 21
3104413 TAAATTATGT
* *
3104423 ATGATTTATTATTAAGTTATA
1 ATGATTAACTATTAAGTTATA
*
3104444 ATTGATTAACTATTATGTTATA
1 A-TGATTAACTATTAAGTTATA
* * *
3104466 GATGATTCACTACTAAATTATA
1 -ATGATTAACTATTAAGTTATA
* * * * *
3104488 TTAATTTACTTTTTAAGTTTTTA
1 ATGATTAAC-TATTAAG-TTATA
3104511 ATGATTAAC
1 ATGATTAAC
3104520 AACTAAATTA
Statistics
Matches: 55, Mismatches: 17, Indels: 6
0.71 0.22 0.08
Matches are distributed among these distances:
21 7 0.13
22 37 0.67
23 11 0.20
ACGTcount: A:0.36, C:0.06, G:0.08, T:0.49
Consensus pattern (21 bp):
ATGATTAACTATTAAGTTATA
Found at i:3104546 original size:22 final size:22
Alignment explanation
Indices: 3104521--3104562 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
3104511 ATGATTAACA
*
3104521 ACTAAATTATTATTTATTTAAT
1 ACTAAATTATTATTAATTTAAT
**
3104543 ACTATTTTATTATTAATTTA
1 ACTAAATTATTATTAATTTA
3104563 TCACTGTCAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.57
Consensus pattern (22 bp):
ACTAAATTATTATTAATTTAAT
Found at i:3104624 original size:22 final size:22
Alignment explanation
Indices: 3104599--3104711 Score: 75
Period size: 22 Copynumber: 5.1 Consensus size: 22
3104589 TGAAACTGAC
*
3104599 TTACTATTAAATTATTATTAAT
1 TTACTATTAAATTATCATTAAT
* *
3104621 TTACTATTAAGTTATCATTCAT
1 TTACTATTAAATTATCATTAAT
* * * *
3104643 TTATTACTAAGTTATCAATAAT
1 TTACTATTAAATTATCATTAAT
* * **
3104665 TAATTACAAAATTATCACTT-AT
1 TTACTATTAAATTATCA-TTAAT
** * *
3104687 TTTTTATTAAGTTATCCTTAAT
1 TTACTATTAAATTATCATTAAT
3104709 TTA
1 TTA
3104712 ATACTATACT
Statistics
Matches: 71, Mismatches: 18, Indels: 4
0.76 0.19 0.04
Matches are distributed among these distances:
21 2 0.03
22 68 0.96
23 1 0.01
ACGTcount: A:0.37, C:0.10, G:0.03, T:0.50
Consensus pattern (22 bp):
TTACTATTAAATTATCATTAAT
Found at i:3105189 original size:22 final size:22
Alignment explanation
Indices: 3105138--3105189 Score: 52
Period size: 22 Copynumber: 2.3 Consensus size: 22
3105128 TATAATTTTT
*
3105138 TATACTAATATAAATATTAAAAC
1 TATA-TAAAATAAATATTAAAAC
* *
3105161 TAAATAAAATAAATATATATAA-
1 TATATAAAATAAATAT-TAAAAC
3105183 TATATAA
1 TATATAA
3105190 TAAGTCAATC
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
22 17 0.71
23 7 0.29
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.35
Consensus pattern (22 bp):
TATATAAAATAAATATTAAAAC
Found at i:3105380 original size:39 final size:34
Alignment explanation
Indices: 3105307--3105382 Score: 89
Period size: 34 Copynumber: 2.1 Consensus size: 34
3105297 TTTAAGTCAC
*
3105307 TTTTAAATTTAGTTAAATTATAATATATAATAAA
1 TTTTAAATTTAGTTAAATGATAATATATAATAAA
*
3105341 TTTTAAATTTAGATGTAAAGTGATAATTAATATGATAAA
1 TTTTAAATTTAG-T-TAAA-TGATAA-T-ATATAATAAA
3105380 TTT
1 TTT
3105383 CAATTCTTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
34 12 0.34
35 1 0.03
36 4 0.11
37 5 0.14
38 1 0.03
39 12 0.34
ACGTcount: A:0.46, C:0.00, G:0.08, T:0.46
Consensus pattern (34 bp):
TTTTAAATTTAGTTAAATGATAATATATAATAAA
Found at i:3112854 original size:9 final size:10
Alignment explanation
Indices: 3112834--3112876 Score: 54
Period size: 9 Copynumber: 4.5 Consensus size: 10
3112824 TTGAATTAAA
3112834 TTATATATTT
1 TTATATATTT
*
3112844 TTTTA-ATTT
1 TTATATATTT
3112853 TTATATATTT
1 TTATATATTT
*
3112863 TTA-AAATTT
1 TTATATATTT
3112872 TTATA
1 TTATA
3112877 AAATAAAAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
9 16 0.57
10 12 0.43
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (10 bp):
TTATATATTT
Found at i:3112858 original size:19 final size:19
Alignment explanation
Indices: 3112834--3112876 Score: 68
Period size: 19 Copynumber: 2.3 Consensus size: 19
3112824 TTGAATTAAA
**
3112834 TTATATATTTTTTTAATTT
1 TTATATATTTTTAAAATTT
3112853 TTATATATTTTTAAAATTT
1 TTATATATTTTTAAAATTT
3112872 TTATA
1 TTATA
3112877 AAATAAAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (19 bp):
TTATATATTTTTAAAATTT
Found at i:3112912 original size:24 final size:23
Alignment explanation
Indices: 3112865--3112917 Score: 63
Period size: 24 Copynumber: 2.3 Consensus size: 23
3112855 ATATATTTTT
*
3112865 AAAATTTTTATAAAATAAAAATA
1 AAAATTTATATAAAATAAAAATA
*
3112888 ATAAATTTATATTAAAAT-AATATA
1 A-AAATTTATA-TAAAATAAAAATA
3112912 AAAATT
1 AAAATT
3112918 AAAAATTTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
23 6 0.23
24 14 0.54
25 6 0.23
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (23 bp):
AAAATTTATATAAAATAAAAATA
Found at i:3115331 original size:3 final size:3
Alignment explanation
Indices: 3115323--3115349 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
3115313 CTTATCATGC
3115323 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
3115350 TAAACTGAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:3124286 original size:15 final size:15
Alignment explanation
Indices: 3124266--3124296 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
3124256 AAAGCTTAAT
3124266 ATTTTTAAGATTTTG
1 ATTTTTAAGATTTTG
*
3124281 ATTTTTAATATTTTG
1 ATTTTTAAGATTTTG
3124296 A
1 A
3124297 AGCTCATTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.29, C:0.00, G:0.10, T:0.61
Consensus pattern (15 bp):
ATTTTTAAGATTTTG
Found at i:3131487 original size:93 final size:93
Alignment explanation
Indices: 3131328--3131509 Score: 265
Period size: 93 Copynumber: 2.0 Consensus size: 93
3131318 ATATGTAGAA
* * *
3131328 ATCTAAACCCAAACTTGTAAGGTCTTTTTTATGGGACAAAATCGTGAAACCTTCATATCAAAGCA
1 ATCTAAACCCAAACTTATAAGGTCTTTTTTATGAGACAAAACCGTGAAACCTTCATATCAAAGCA
3131393 GACAATACCTCATAGGTTAGGTGTAAAG
66 GACAATACCTCATAGGTTAGGTGTAAAG
* * * * *
3131421 ATCTAAACCTAAACTTATGAGGTCTTTTTTGTGAGATAAAACCGTGAGACCTTCATATCAAAGCA
1 ATCTAAACCCAAACTTATAAGGTCTTTTTTATGAGACAAAACCGTGAAACCTTCATATCAAAGCA
** *
3131486 GACAATACCTTGTAGGTTGGGTGT
66 GACAATACCTCATAGGTTAGGTGT
3131510 TGGTCTCCAC
Statistics
Matches: 78, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
93 78 1.00
ACGTcount: A:0.34, C:0.18, G:0.19, T:0.30
Consensus pattern (93 bp):
ATCTAAACCCAAACTTATAAGGTCTTTTTTATGAGACAAAACCGTGAAACCTTCATATCAAAGCA
GACAATACCTCATAGGTTAGGTGTAAAG
Found at i:3142524 original size:184 final size:185
Alignment explanation
Indices: 3142280--3142631 Score: 607
Period size: 184 Copynumber: 1.9 Consensus size: 185
3142270 TTTTTTTGTC
* *
3142280 TACACTCTTTCTGAAATATTAAATTTTAAAAAAAAATTGATAGTGATTTGTTAAGCAAAGAATAA
1 TACACTCTTTCTGAAATATTAAATTTTAAAAAAAAATTGATAGTGATCTATTAAGCAAAGAATAA
* * *
3142345 ATCATGTTGATTGCTTCATCCTATAATGGCTTTTGTAATTTTACCATTCTCAATATACATTTGAC
66 ATCATGTTGATTGCTTCATCCTAGAATAGCTTTTGTAATTTTACCATCCTCAATATACATTTGAC
*
3142410 TTTTTTCACAATGGTGCGGTTCATCTTTTTAGCTATACTGTAATGTTTCAAGTTT
131 TTATTTCACAATGGTGCGGTTCATCTTTTTAGCTATACTGTAATGTTTCAAGTTT
* * *
3142465 TACACTTTTTTTGAAATATTAAATTTT-AAAAAAAATTGATGGTGATCTATTAAGCAAAGAATAA
1 TACACTCTTTCTGAAATATTAAATTTTAAAAAAAAATTGATAGTGATCTATTAAGCAAAGAATAA
3142529 ATCATGTTGATTGCTTCATCCTAGAATAGCTTTTGTAATTTTACCATCCTCAATATACATTTGAC
66 ATCATGTTGATTGCTTCATCCTAGAATAGCTTTTGTAATTTTACCATCCTCAATATACATTTGAC
*
3142594 TTATTTCATAATGGTGCGGTTCATCTTTTTAGCTATAC
131 TTATTTCACAATGGTGCGGTTCATCTTTTTAGCTATAC
3142632 CATTATACTG
Statistics
Matches: 157, Mismatches: 10, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
184 132 0.84
185 25 0.16
ACGTcount: A:0.32, C:0.14, G:0.12, T:0.42
Consensus pattern (185 bp):
TACACTCTTTCTGAAATATTAAATTTTAAAAAAAAATTGATAGTGATCTATTAAGCAAAGAATAA
ATCATGTTGATTGCTTCATCCTAGAATAGCTTTTGTAATTTTACCATCCTCAATATACATTTGAC
TTATTTCACAATGGTGCGGTTCATCTTTTTAGCTATACTGTAATGTTTCAAGTTT
Found at i:3143211 original size:186 final size:185
Alignment explanation
Indices: 3142898--3143253 Score: 667
Period size: 186 Copynumber: 1.9 Consensus size: 185
3142888 TTTTTTTTTG
3142898 TCTACACTCTTTCTGAAATATTAAATTTAAAAAAAAAATTGATGGTGATCTGTTAAGCAAAGAAT
1 TCTACACTCTTTCTGAAATATTAAATTTAAAAAAAAAATTGATGGTGATCTGTTAAGCAAAGAAT
* *
3142963 AAATCATGTTGATTGCTTCATCCTAGAATGGCTTTTGTAATTTTACCATCTTCAATATACATTTG
66 AAATCATGTTGATTGCTTCATCCTAGAATGGCTTTTGTAATTATACCATCCTCAATATACATTTG
3143028 ACTTTTTTCACAATGGTGCGGTTCATCTTTTTAGCTATACTGTAATGTTTCAGGT
131 ACTTTTTTCACAATGGTGCGGTTCATCTTTTTAGCTATACTGTAATGTTTCAGGT
*
3143083 TCTACACTCTTTTCTGAAATATTAAATTTTAAAAAAAAATTGATGGTGATCTGTTAAGCAAAGAA
1 TCTACACTC-TTTCTGAAATATTAAATTTAAAAAAAAAATTGATGGTGATCTGTTAAGCAAAGAA
3143148 TAAATCATGTTGATTGCTTCATCCTAGAATGGCTTTTGTAATTATACCATCCTCAATATACATTT
65 TAAATCATGTTGATTGCTTCATCCTAGAATGGCTTTTGTAATTATACCATCCTCAATATACATTT
*
3143213 GACTTTTTTCATAATGGTGCGGTTCATCTTTTTAGCTATAC
130 GACTTTTTTCACAATGGTGCGGTTCATCTTTTTAGCTATAC
3143254 CATTATACTG
Statistics
Matches: 166, Mismatches: 4, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
185 9 0.05
186 157 0.95
ACGTcount: A:0.31, C:0.15, G:0.13, T:0.40
Consensus pattern (185 bp):
TCTACACTCTTTCTGAAATATTAAATTTAAAAAAAAAATTGATGGTGATCTGTTAAGCAAAGAAT
AAATCATGTTGATTGCTTCATCCTAGAATGGCTTTTGTAATTATACCATCCTCAATATACATTTG
ACTTTTTTCACAATGGTGCGGTTCATCTTTTTAGCTATACTGTAATGTTTCAGGT
Found at i:3143306 original size:622 final size:618
Alignment explanation
Indices: 3142127--3143363 Score: 2253
Period size: 622 Copynumber: 2.0 Consensus size: 618
3142117 CATTAGATCC
3142127 TATACCCTATAATCAAATTTCTCATCATCATATCTTATAAATACACACTGTATGGCTTTACTATC
1 TATACCCTATAATCAAATTTCTCATCATCATATCTTATAAATACACACTGTATGGCTTTACTATC
*
3142192 AAGCTTTGATCATTGTTCTTTCGGTACATGTATAAATATTTTACACCCAAAGACTTTCAAGTAAG
66 AAGCTTTGATCATTGTTCTTTCGGTACATGCATAAATATTTTACACCCAAAGACTTTCAAGTAAG
*
3142257 AGTATAAAGTATTTTTTTTTGTCTACACTCTTTCTGAAATATTAAATTTTAAAAAAAAATTGATA
131 AGTATAAAGTATTTTTTTTTGTCTACACTCTTTCTGAAATATTAAATTTAAAAAAAAAATTGATA
* *
3142322 GTGATTTGTTAAGCAAAGAATAAATCATGTTGATTGCTTCATCCTATAATGGCTTTTGTAATTTT
196 GTGATCTGTTAAGCAAAGAATAAATCATGTTGATTGCTTCATCCTAGAATGGCTTTTGTAATTTT
3142387 ACCATTCTCAATATACATTTGACTTTTTTCACAATGGTGCGGTTCATCTTTTTAGCTATACTGTA
261 ACCATTCTCAATATACATTTGACTTTTTTCACAATGGTGCGGTTCATCTTTTTAGCTATACTGTA
* *
3142452 ATGTTTCAAGTTTTACACTTTTTTTGAAATATTAAATTTTAAAAAAAATTGATGGTGATCTATTA
326 ATGTTTCAAGTTCTACACTTTTTCTGAAATATTAAATTTTAAAAAAAATTGATGGTGATCTATTA
*
3142517 AGCAAAGAATAAATCATGTTGATTGCTTCATCCTAGAATAGCTTTTGTAATTTTACCATCCTCAA
391 AGCAAAGAATAAATCATGTTGATTGCTTCATCCTAGAATAGCTTTTGTAATTATACCATCCTCAA
3142582 TATACATTTGACTTATTTCATAATGGTGCGGTTCATCTTTTTAGCTATACCATTATACTGTAATG
456 TATACATTTGACTTATTTCATAATGGTGCGGTTCATCTTTTTAGCTATACCATTATACTGTAATG
3142647 TTTCAGGTTTTATCATCCCATGCCTGATCTCATACTTTGAATAATATTTTTCAAAGTTTTTAGAT
521 TTTCAGGTTTTATCATCCCATGCCTGATCTCATACTTTGAATAATATTTTTCAAAGTTTTTAGAT
3142712 GTGTATTTTGTACCATTATCAGTTCAAATATCT
586 GTGTATTTTGTACCATTATCAGTTCAAATATCT
* *
3142745 TATACCCTGTAATCAAATTTTTCATCATCATATCTTATAAATACACACTGTATGGCTTTACTATC
1 TATACCCTATAATCAAATTTCTCATCATCATATCTTATAAATACACACTGTATGGCTTTACTATC
*
3142810 AAGCTTTGATCATTGTTTTTTCGGTACATGCATAAATATTTTACACCCAAAGACTTTCAAGTAAG
66 AAGCTTTGATCATTGTTCTTTCGGTACATGCATAAATATTTTACACCCAAAGACTTTCAAGTAAG
3142875 AGTATAAAGTATTTTTTTTTTTGTCTACACTCTTTCTGAAATATTAAATTTAAAAAAAAAATTGA
131 AGTATAAAGTA--TTTTTTTTTGTCTACACTCTTTCTGAAATATTAAATTTAAAAAAAAAATTGA
*
3142940 TGGTGATCTGTTAAGCAAAGAATAAATCATGTTGATTGCTTCATCCTAGAATGGCTTTTGTAATT
194 TAGTGATCTGTTAAGCAAAGAATAAATCATGTTGATTGCTTCATCCTAGAATGGCTTTTGTAATT
3143005 TTACCA-TCTTCAATATACATTTGACTTTTTTCACAATGGTGCGGTTCATCTTTTTAGCTATACT
259 TTACCATTC-TCAATATACATTTGACTTTTTTCACAATGGTGCGGTTCATCTTTTTAGCTATACT
*
3143069 GTAATGTTTCAGGTTCTACACTCTTTTCTGAAATATTAAATTTTAAAAAAAAATTGATGGTGATC
323 GTAATGTTTCAAGTTCTACACT-TTTTCTGAAATATTAAATTTT-AAAAAAAATTGATGGTGATC
* *
3143134 TGTTAAGCAAAGAATAAATCATGTTGATTGCTTCATCCTAGAATGGCTTTTGTAATTATACCATC
386 TATTAAGCAAAGAATAAATCATGTTGATTGCTTCATCCTAGAATAGCTTTTGTAATTATACCATC
*
3143199 CTCAATATACATTTGACTTTTTTCATAATGGTGCGGTTCATCTTTTTAGCTATACCATTATACTG
451 CTCAATATACATTTGACTTATTTCATAATGGTGCGGTTCATCTTTTTAGCTATACCATTATACTG
*
3143264 TAATGTTTCA-GTTTCTATCATCCCATGCCTGATCTTATACTTTGAATAATATTTTTCAAAGTTT
516 TAATGTTTCAGGTTT-TATCATCCCATGCCTGATCTCATACTTTGAATAATATTTTTCAAAGTTT
*
3143328 TTAGATGTGTATTTTGTACCATTATCAGTTTAAATA
580 TTAGATGTGTATTTTGTACCATTATCAGTTCAAATA
3143364 CACTTAAAGG
Statistics
Matches: 596, Mismatches: 17, Indels: 8
0.96 0.03 0.01
Matches are distributed among these distances:
618 137 0.23
619 2 0.00
620 194 0.33
621 24 0.04
622 239 0.40
ACGTcount: A:0.31, C:0.15, G:0.12, T:0.42
Consensus pattern (618 bp):
TATACCCTATAATCAAATTTCTCATCATCATATCTTATAAATACACACTGTATGGCTTTACTATC
AAGCTTTGATCATTGTTCTTTCGGTACATGCATAAATATTTTACACCCAAAGACTTTCAAGTAAG
AGTATAAAGTATTTTTTTTTGTCTACACTCTTTCTGAAATATTAAATTTAAAAAAAAAATTGATA
GTGATCTGTTAAGCAAAGAATAAATCATGTTGATTGCTTCATCCTAGAATGGCTTTTGTAATTTT
ACCATTCTCAATATACATTTGACTTTTTTCACAATGGTGCGGTTCATCTTTTTAGCTATACTGTA
ATGTTTCAAGTTCTACACTTTTTCTGAAATATTAAATTTTAAAAAAAATTGATGGTGATCTATTA
AGCAAAGAATAAATCATGTTGATTGCTTCATCCTAGAATAGCTTTTGTAATTATACCATCCTCAA
TATACATTTGACTTATTTCATAATGGTGCGGTTCATCTTTTTAGCTATACCATTATACTGTAATG
TTTCAGGTTTTATCATCCCATGCCTGATCTCATACTTTGAATAATATTTTTCAAAGTTTTTAGAT
GTGTATTTTGTACCATTATCAGTTCAAATATCT
Found at i:3145070 original size:3 final size:3
Alignment explanation
Indices: 3145062--3145142 Score: 90
Period size: 3 Copynumber: 27.0 Consensus size: 3
3145052 AACTATTACC
* * * * *
3145062 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT GTT GTT GTT GTT GTT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* * *
3145110 GTT GTT ATT ATT ATT ATT ACT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
3145143 TTCTTTATGT
Statistics
Matches: 74, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 74 1.00
ACGTcount: A:0.25, C:0.01, G:0.09, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:3145962 original size:7 final size:6
Alignment explanation
Indices: 3145946--3146002 Score: 60
Period size: 6 Copynumber: 9.0 Consensus size: 6
3145936 GAATCGCATG
* * *
3145946 TTTTTC TTTTTA TTTTTA TTTTTA TTTTCATC TTTTTA TTTTGA TTTTTGA
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTT--TA TTTTTA TTTTTA TTTTT-A
3145997 TTTTTA
1 TTTTTA
3146003 CTGGTTTTAT
Statistics
Matches: 43, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
6 32 0.74
7 6 0.14
8 5 0.12
ACGTcount: A:0.14, C:0.05, G:0.04, T:0.77
Consensus pattern (6 bp):
TTTTTA
Found at i:3145980 original size:26 final size:27
Alignment explanation
Indices: 3145950--3146000 Score: 86
Period size: 26 Copynumber: 1.9 Consensus size: 27
3145940 CGCATGTTTT
*
3145950 TCTTTTTATTTTTATTTTT-ATTTTCA
1 TCTTTTTATTTTGATTTTTGATTTTCA
3145976 TCTTTTTATTTTGATTTTTGATTTT
1 TCTTTTTATTTTGATTTTTGATTTT
3146001 TACTGGTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 18 0.78
27 5 0.22
ACGTcount: A:0.14, C:0.06, G:0.04, T:0.76
Consensus pattern (27 bp):
TCTTTTTATTTTGATTTTTGATTTTCA
Found at i:3152933 original size:35 final size:35
Alignment explanation
Indices: 3152887--3152972 Score: 111
Period size: 35 Copynumber: 2.5 Consensus size: 35
3152877 ACAAAAAGTC
* * *
3152887 TTTGAATTATAATTAAAAAATTATTTAAGTTTTTA
1 TTTGTATTATAATTAAAAAATTATTTAAATATTTA
* * *
3152922 TTTTTATTATAATTAATAAATTTTTTAAATATTTA
1 TTTGTATTATAATTAAAAAATTATTTAAATATTTA
3152957 TTTGTATT-TAATTAAA
1 TTTGTATTATAATTAAA
3152973 TTTTCATTTA
Statistics
Matches: 43, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
34 7 0.16
35 36 0.84
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (35 bp):
TTTGTATTATAATTAAAAAATTATTTAAATATTTA
Found at i:3153650 original size:15 final size:17
Alignment explanation
Indices: 3153630--3153671 Score: 54
Period size: 15 Copynumber: 2.6 Consensus size: 17
3153620 AATTTATAAA
3153630 ATTATTTTAA-AAA-AT
1 ATTATTTTAATAAATAT
3153645 ATTA-TTTAATAAATAT
1 ATTATTTTAATAAATAT
*
3153661 ATAATTTTAAT
1 ATTATTTTAAT
3153672 TTTAATATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 5 0.22
15 7 0.30
16 5 0.22
17 6 0.26
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
ATTATTTTAATAAATAT
Found at i:3153983 original size:16 final size:18
Alignment explanation
Indices: 3153962--3153998 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
3153952 ATTATCATTT
3153962 TTTAAAGT-TT-ATATAA
1 TTTAAAGTATTGATATAA
*
3153978 TTTAAATTATTGATATAA
1 TTTAAAGTATTGATATAA
3153996 TTT
1 TTT
3153999 TTAAAAATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 7 0.39
17 2 0.11
18 9 0.50
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (18 bp):
TTTAAAGTATTGATATAA
Found at i:3154703 original size:22 final size:23
Alignment explanation
Indices: 3154678--3154723 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
3154668 CAAGAACATG
3154678 AAAAGAAA-AAAAGGGAAAAAAA
1 AAAAGAAATAAAAGGGAAAAAAA
* *
3154700 AAAAGAAATAAATGGGAAGAAAA
1 AAAAGAAATAAAAGGGAAAAAAA
3154723 A
1 A
3154724 GTCAACCAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 8 0.38
23 13 0.62
ACGTcount: A:0.76, C:0.00, G:0.20, T:0.04
Consensus pattern (23 bp):
AAAAGAAATAAAAGGGAAAAAAA
Found at i:3155954 original size:26 final size:26
Alignment explanation
Indices: 3155924--3155978 Score: 92
Period size: 26 Copynumber: 2.1 Consensus size: 26
3155914 TTTTCATTAT
*
3155924 TTAAAAATTTAATTCAATTGATTCAA
1 TTAAAAATTTAATTCAATTAATTCAA
*
3155950 TTAAAAATTTAATTCAATTAATTTAA
1 TTAAAAATTTAATTCAATTAATTCAA
3155976 TTA
1 TTA
3155979 TACATAAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.47, C:0.05, G:0.02, T:0.45
Consensus pattern (26 bp):
TTAAAAATTTAATTCAATTAATTCAA
Found at i:3155972 original size:21 final size:23
Alignment explanation
Indices: 3155919--3155967 Score: 62
Period size: 26 Copynumber: 2.0 Consensus size: 23
3155909 AGAAGTTTTC
*
3155919 ATTATTTAAAAATTTAATTCAATT
1 ATTAATTAAAAATTTAATTCAA-T
3155943 GATTCAATTAAAAATTTAATTCAAT
1 -ATT-AATTAAAAATTTAATTCAAT
3155968 TAATTTAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 4 0.18
26 18 0.82
ACGTcount: A:0.47, C:0.06, G:0.02, T:0.45
Consensus pattern (23 bp):
ATTAATTAAAAATTTAATTCAAT
Found at i:3156076 original size:2 final size:2
Alignment explanation
Indices: 3156069--3156108 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
3156059 ATTTTCTTTT
*
3156069 TA TA TA TA TA AA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3156109 CACATATAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:3158107 original size:24 final size:21
Alignment explanation
Indices: 3158051--3158107 Score: 51
Period size: 24 Copynumber: 2.5 Consensus size: 21
3158041 TTTAAATTTT
*
3158051 ATTTAATATATTTTTTTATTA
1 ATTTAATAAATTTTTTTATTA
* *
3158072 ATTCAAACAAATTTATTTATATTAA
1 ATT-TAATAAATTT-TTT-TATT-A
3158097 ATTTAATAAAT
1 ATTTAATAAAT
3158108 CCATAAAAAA
Statistics
Matches: 27, Mismatches: 5, Indels: 5
0.73 0.14 0.14
Matches are distributed among these distances:
21 3 0.11
22 7 0.26
23 3 0.11
24 10 0.37
25 4 0.15
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.53
Consensus pattern (21 bp):
ATTTAATAAATTTTTTTATTA
Found at i:3158469 original size:11 final size:11
Alignment explanation
Indices: 3158453--3158489 Score: 56
Period size: 11 Copynumber: 3.4 Consensus size: 11
3158443 GAGCGTAACC
*
3158453 TTTCTTTTTGT
1 TTTCTTTTTTT
3158464 TTTCTTTTTTT
1 TTTCTTTTTTT
*
3158475 TTTTTTTTTTT
1 TTTCTTTTTTT
3158486 TTTC
1 TTTC
3158490 CAGTTAAGTC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.00, C:0.08, G:0.03, T:0.89
Consensus pattern (11 bp):
TTTCTTTTTTT
Found at i:3171403 original size:2 final size:2
Alignment explanation
Indices: 3171396--3171424 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3171386 ATGTTCTAAC
3171396 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3171425 TTGTTTCAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3181210 original size:24 final size:25
Alignment explanation
Indices: 3181166--3181224 Score: 77
Period size: 24 Copynumber: 2.4 Consensus size: 25
3181156 TATTATATAG
*
3181166 ATAAT-TCAAAATATTCATCAAATT
1 ATAATGTCAAAATATTCATCAAATC
*
3181190 ATAATGTCAAAATATT-TTCAAATC
1 ATAATGTCAAAATATTCATCAAATC
*
3181214 ATCATGTCAAA
1 ATAATGTCAAA
3181225 CATTTCGTAG
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
24 21 0.68
25 10 0.32
ACGTcount: A:0.47, C:0.14, G:0.03, T:0.36
Consensus pattern (25 bp):
ATAATGTCAAAATATTCATCAAATC
Done.